Please provide more details about the platform you are using, specifically the operating system and file system.
With regards to Linux, it's most likely going to be stored as a UTC timestamp (see Jim's answer).
On Windows, if you are using NTFS then you are going to find similar behavior as Linux in that the timestamp is based on UTC. But they use different epoch times. When stored as an integer on Linux,
1/1/1970. But on Windows,
If you are using FAT or FAT32 on Windows, then beware that file times are not based on UTC, but on the local time zone of the computer that recorded it. That means there can be ambiguity around daylight saving time transition dates, and if you change your time zone, or bring files to a computer in a different time zone (perhaps over a FAT32-formatted USB key, for example) that the times will be interpreted as if they were in that time zone.
You can read more about Windows specifics here.
Either way, the ticking of the clock, or the manual adjustment of the clock, will not affect timestamps of recorded files in any way. It will only affect timestamps of new files.