I have made a room automation with a arduino uno and few IR sensors. Now I want to replace my arduino uno with a arduino nano V3. Do I have to change all the program? Or would I have to face some other problems?
YES YOU CAN!!!!! Aka, don't shout please.
The Nano and Uno are both based around the same micro controller so you can just swap them. Only difference is the Nano still uses the old bootloader (which you can replace if you want to) so it will upload a bit slower. After that, no difference at all.
The Nano has a poor 3.3volt power supply (c. 50mA depending on its type - Chinese clone, original etc.) But other than that, there should be few differences.
I'm now experimenting with a library (dfc77 - radio time signal clock ) which has a hardware spec. which rules out a Nano because it [the Nano] has only a resonator, not a real crystal. Such applications are, however, rare.
But in China you can buy Nano's with crystal as well :)
Also, keep in mind that the Nano does have the USB connector and the Pro Mini does not. Also, and I know this is obvious, the Nano doesn't accept a standard Arduino shield.