I'm thinking of using a 5V and 2.5Amp power supply to power up my Raspberrypi 3 model B over it's GPIO 5V PIN. Is it safe to use 5V 2A IN GPIO PIN?
You can power the Pi using the 5V and ground pins on the expansion header.
Please note that the power and ground pins are NOT GPIO and it is wrong to refer to them as such.
See https://pinout.xyz/ for details of the pins on the expansion header.
The amperage of your 5V power supply doesn't matter as long as it is enough to power the Pi and connected peripherals. For safety it might be sensible to add a 2.5 amp fuse to your circuit (not to protect the Pi, to protect things connected to the Pi).