I agree with all of the others - they mean 2am, 3am, possibly even 4am. Are you reading "Little Women"? That's a wonderful book!

I agree with marc on this. Way past midnight!

當Marmee回來（回家）的時候，早就過了午夜

It just means it was a lot later than midnight when Marmee returned. You could also use 'way past' in place of 'Long past' here. Hope this helps

It wasn't just a minute or two past midnight. It wasn't 12:05 or 12:10 or even 1 a.m. It was long past midnight, hours past midnight. It might have been 1:00 am, 2:00 am, 3:00 am. If you were sitting in the living room waiting for Marmee to return, you might well have fallen asleep, and awakened when she returned. You might not know exactly what time it was, only that it was long past midnight.