What is the unit of time on the Voyager Golden Record? What is the unit of time on the Voyager Golden Record?
Apparently, it has something to do with "a fundamental transition of the hydrogen atom".
A high-level description was provided by NASA, as shown in this answer.
How will the aliens know what this means?
 A: To add to John Rennie's answer and Hennes's Answer, an answer to your last sentence: 

How will the aliens know what this means?

is well given in a thoroughly interesting and enjoyable tale by Carl Sagan's novel Contact. I can't recall whether the following is made clear in the film with Jodie Foster. 
In the novel, signals received from the Vega system is an out-of-Earth culture's equivalent of the Voyager's golden record. In particular, Sagan describes in great detail how this culture has highly thoughtfully arranged things so that humans will recognise the signal as that from an intelligent civilisation, and moreover be able to decode it with no knowledge of that culture. The concepts of integer and prime number, which are universal and independent of culture, was used to achieve this:


*

*The signal's global structure was a repeating sequence of 26 otherwise unrelated large prime numbers. The universality of integers and primes allows a human reader ken that this is something very special, and the otherwise random relationship between the primes makes it unlikely this is anything other than a purposeful message;

*Further analysis of the signals fine structure shows that it comprises a huge number of basic units, perhaps letters. Moreover, this huge number is the product of three primes. So it is not much of a stretch to conclude that the message is a rank three array. Presumably, the alien culture perceives three spatial dimensions as we do, so there are two simple candidates for what a rank 3 array of symbols might be conveying: (1) a sequence of two dimensional still pictures, or (2) a three dimensional still. In the first instance of the message, the message was a retransmission of Adolf Hitler's opening speech of the 1936 olympics, thus letting us know that the other culture had intercepted our transmissions into space and had understood them to some degree. In the second instance of the message, the message was a three dimensional blueprint for a machine that would transport humans to Vega and thus allow contact.
A: Because physics is the same for both us and for anything which might be out there. 
If we use basic things like the transitions in hydrogen atoms, prime numbers etc. then no matter who or where you are you can interpreted these basic things.
And while hydrogen might seem complicated to us, it is one of the most abundant elements in the universe and its properties will be well known by anyone able to examine a spacecraft.
A: In a  neutral hydrogen atom the ground state has the electron and proton spins anti-parallel i.e. lined up with each other but pointing in opposite directions. The state with the spins parallel and pointing in the same direction has a slightly higher energy, and transitions between these two states produce the notorious 21cm hydrogen line.

Since the hydrogen 21cm emission is detectable everywhere the idea is that any aliens will know what it is and will be able to guess that's what the diagram means. The frequency of this oscillation is 1420.40575177 MHz, so the period is 0.704ns and that is the time unit you're referring to.
