Is it okay that my supervisor insists for me to work from my room at night? I am a female PhD student in the end of my second year, and my supervisor has been acting weird lately. He asks me to run the experiments from my laptop and not from my PC in the lab (it does not affect the test), and he does that when it's 11 or 12 at night.
We usually do a voice call to discuss work, but very recently he asked for a video call and it was late at night… and just today he insisted that I work from my room and not from the lab.

I just want to know what you guys think. I don't know if it's a culture difference thing or that I should really be careful. I think it's really weird considering that I've been working with him for two years and he wasn't even nice to me.
This sets off all kind of red flags. In the absence of an extremely good rationale, this is very strange and entirely unacceptable. I would recommend that you make an appointment with your graduate program director and discuss the situation ASAP. That person will have more background about the situation and more perspective, and can offer you better advice than we can here.