時間に is used when you want to do something at some time. Or when the time is describing some other subject.

Please go out when it is time. 時間になったら出てください。Going out is the subject, time is just describing when you need to go out.

Meet me at this time. この時間に会ってください。 Meeting is the subject of this sentence; time is describing when this should be happening.


時間は is talking about the current situation. Or when the time is the subject.

The time is 5 o'clock 時間は５時です。The time is the subject, and five o'clock is the adjective describing the time.

There isn't much time left. 時間はあまり残ってない。The time is once again the subject, he lack of time describes it.