Can mechanical work change thermal energy? As stated by @Mark Eichenlaub in this link heat is the energy transferred between two systems by means aside from work. But then when you pull the brakes in your car, the tires, the road everything becomes hotter aka they gain thermal energy. Here, the car is doing work on the road.But the road doesn't gain 100% energy of the work done.Some of the energy is 'lost' to the environment as heat. But if  some thermal energy is lost to the environment, then there must be some other amount of thermal energy transferred to the roads, bcz otherwise they wouldn't gain thermal energy . My assumption is this thermal energy is gained via the actual mechanical work done by the car on the road. So, some amount of energy of the total work done by the car is used to actually move the car forward on the road. But there is some other amount of energy that is used to 'heat up' the road. Note that this is all my assumption. I'm not 100℅ sure about this. And So, this is essentially my question.
Can thermal(putting extra stress on the word 'thermal' bcz the internal energy aka sum of all energies of a system that isn't due to an external force is obviously going to increase when work is done on the system, but I am asking explicitly about the thermal energy) energy change by means other than heat( let's say when mechanical work is done on the system)
 A: 
Can thermal energy change by means other than heat( let's say when mechanical work is done on the system)

Absolutely. This is the subject of Joule's famous 1850 paper entitled "The Mechanical Equivalent of Heat". With careful measurements of the work done on a system and careful measurements of the temperature of the system he was able to show that mechanical work was proportional to heat.
It turns out that this is a general principle. For example, not only mechanical work but electrical work can also change thermal energy. As far as I know, all forms of work can be used to produce a change in thermal energy.
However, I am a little concerned about your example:

when you pull the brakes in your car, the tires, the road everything becomes hotter aka they gain thermal energy. Here, the car is doing work on the road. But the road doesn't gain 100% energy of the work done.

A car does very little work on a road while braking, ideally it does no work on the road. The work is done on brake shoes and pads, and almost all of the energy is dissipated into the material of the brakes themselves. Due to deformation of the road there is some work done on the road itself, but it is very small. The tires do get warm and do transfer heat to the road, but that is also a very small percentage compared to the work done in the brakes themselves.
A: 
Can thermal....energy change by means other than heat( let's say when
mechanical work is done on the system)

If by "thermal energy" you are referring to internal energy, then yes internal energy can change by means other than heat. It can change by the same amount by doing an equal amount of work, since the change in internal energy is related to heat and work by the first law:
$$\Delta U=Q-W$$
where $Q$ is is  positive if heat transfers to the system and $W$ is positive if work is done by the system.
For example, in the case of an ideal gas where internal energy depends only on temperature, you can increase the temperature of the gas with heat with no work, or by doing work (compressing the gas) with no heat (compressing it adiabatically). The end result is the same increase in temperature and the same increase in internal energy.

But then when you pull the brakes in your car, the tires, the road
everything becomes hotter aka they gain thermal energy.

In the case of disc brakes, when you step on the brakes the main things that get hot (experience a substantial increase in temperature) are the brake pads (which are stationary) and the rotors (which are attached to and rotate with the wheels) due to kinetic friction between them.
In effect, the majority of the loss of macroscopic kinetic energy of the vehicle (kinetic energy of the vehicle as a whole when it decelerates) is converted to microscopic kinetic energy (an increase in the molecular kinetic energy of the brake materials which results in an increase in temperature), and thus the internal kinetic energy of the brake materials.
The actual slowing down of the vehicle during braking is the result of the counter-clockwise torque that the brakes apply to the wheels. The force of that torque acting forward on the ground is opposed by the equal and opposite static friction force that the ground exerts backwards on the vehicle per Newton's third law. This backwards force, neglecting air resistance, is the only external force acting backwards on the vehicle and is thus responsible for decelerating the vehicle.
Now (ignoring rolling resistance), there are no frictional losses at the contact surfaces between the ground and the tire as long as the maximum possible static friction force is not exceeded so that the vehicle skids on the ground. So as long as the vehicle doesn't skid, the only transfer of energy in the form of heat to the ground would be in the form of heat conduction from the brake materials to the ground.
Eventually, the elevated temperatures of the brake materials relative to their environment (other materials in the vehicle and its environment including the ground) will result in energy transfer in the form of heat to the environment.
Hope this helps.
