Here is some info I found on this topic.
The 365 days per year was probably from direct observation.
Every day was the rotation of the Earth and counting the number of days until the Star Constellations looked the same would be 365 (or 366) days.
The 12 months was an artificial decision because the number of 13 was considered an unlucky number. The observation of the Moon would result in a 28 day "month". But 13 of those lunar months would come close to 365 days (13 * 28 = 364). But no one wanted 13 months so they made it 12 months with 28, 30 or 31 days in each month.
The 24 hours per day came from ancient Egyptians.
They divided the daylight into 12 segments using a crude sun dial.
And then they applied another 12 segments to the night hours.
The 60 minutes per hour and 69 seconds per minute is explained in this write up about the Babylonians.
The division of the hour into 60 minutes and of the minute into 60 seconds comes from the Babylonians who used a sexagesimal (counting in 60s) system for mathematics and astronomy. They derived their number system from the Sumerians who were using it as early as 3500 BC. The use of 12 subdivisions for day and night, with 60 for hours and minutes, turns out to be much more useful than (say) 10 and 100 if you want to avoid having to use complicated notations for parts of a day. Twelve is divisible by two, three, four, six and 12 itself - whereas 10 has only three divisers - whole numbers that divide it a whole number of times. Sixty has 12 divisers and because 60 = 5 x 12 it combines the advantages of both 10 and 12. In fact both 12 and 60 share the property that they have more divisers than any number smaller than themselves. This doesn't, of course, explain how this system spread throughout the world.
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