Since the description said that it would fly at 1:00, I did not regard it as the midnight but the daytime. 聼起來自然嗎?

Yes you can, but this example is awkward and should use other words.
"did not assume it was midnight, but the afternoon" or "did not presume it was midnight" or "did not expect it to be midnight".
Regard ex:
I don't regard you as a peer.
I don't regard you as an enemy, but as a friend.
I did not regard him as an enemy, but as a friend.

Regard is how you see something. Here you are talking about what you concluded they meant when they said 1:00. The difference is slight but important.