Since there is no absolute starting point for time, nor any absolute standard unit for it, you would definitely need some reference point for when you're counting from and how long each unit of time is.
Origin of a timekeeping system
All species would have to have originated from somewhere. This is most likely to be a planet of course, but it can be a space construct in fantasy setting. If it is a planet, then that planet will have a day-night cycle, or in the absence of such a cycle, will have a yearly cycle. Having the amount of time in a year as a starting point and having to have subdivisions to count smaller intervals, they would already have a system of timekeeping.
Without any reason to change it (since time intervals don't change), I assume any civilization that leaves its homeworld would just use the same date/time system. It's familiar to them, computers and mathematical systems would already work with it - it's one of those "if it ain't broke, don't fix it" cases.
Reasons to change it
However, it may be problematic in some cases. For example, you might need a way to compensate for clock drift or be able to determine not only where you are but when you are, if there is a chance your systems are drifting or you need to identify how much time has passed from an event. There would be 2 ways to accomplish this, one being dead reckoning based on what position you think you're in (you check the stars around you, compensate for your movement and see how they've moved, which, assuming your theories about orbital and stellar mechanics are correct, could give you a length of time) and the other would be to have multiple accurate clocks and compare them. Both would probably be used - but is that practical with a date/time system used on a planet?
Probably, since we can just have a format for time and date used for calculations and then change it into a more easily used format for speech (this is what computers do). A long-time space-faring civilization might come up with alternatives, to get over the need to perform complex calculations or constantly compare with their own planet.
A simple change would be to determine what the shortest day is for any planet in the solar system (for planets that are not tidally locked, because those lack a day-night cycle) and use that as the base time unit for days (It might be preferable to not call them days in this case of course). This can be taken further, changing the year length to the amount of time it takes for the closest or farthest terrestrial planet to circle the sun, or the one with the most circular orbit. The intervals for our minutes and seconds could also change - many time units have already been expressed as multiples of Planck time and the same could be done here, albeit with some larger interval instead of the theorized smallest amount of time in the universe.
Of course, this approach would mean that as time goes on and more planets and solar systems are discovered, these times would likely be changed to some other average. Perhaps this species can predict some average times for years, days etc. and create a time/date system that is practical, being easy to use on most worlds.