I have a 3s 2200mah battery. At full charge of two cells it's reading is 4.26v. 4.26v and 4.05v. Per cell. I want to know that what will be the effect on motor performance and it's thrust.
GET A NEW CHARGER you are going to spoil your lipo battery , you should never charge your battery more than 4.20 V per cell they should be as closely balanced as possible . I never charge my lipo more than 4.18 V per cell . The motor would be fine IMO
What effect are you looking for on the motor? Battery voltage determines the rpm of the motor and amps supplied determine the torque.
The motor performance and its thrust does not depend on The voltage of individual cells in a 3cell pack, it only depend on collective voltage. the total voltage of your pack is well above 12v, so motor will have no any performance issues. But your battery is not balanced, means there is chance of destroying your battery.
If you are checking voltage with a multi meter, make sure that your multimeter shows accurate values because many low cost multimeters reading may different than actual (that means 4.26v may be 4.20v & 4.05v is less than that).