If I wake up at 3 am to eat breakfast will I gain weight? I gotta go to work at 4 am And should I count 3 am as my new calories for the day

Yes. You will gain weight if your total calorie intake exceeds the number calories you burn up during the activities of daily living. The time of day or night you ingest the calories is immaterial. More exercise will burn up more calories although reducing the amount of calories you ingest is easier for most people.