An in-wheel motor (IWM) drive system highly integrates the drive motor, deceleration mechanism, and brake, among others, in the wheel, resulting in difficulty dissipating heat. The uneven temperature distribution of the motor is caused by its eccentricity owing to road excitation, tire bounce, and installation errors. This non-uniformity generates thermal stress that endangers motor operation and also causes the motor’s local temperature to increase substantially, thereby affecting its performance. To solve this problem, this study takes a 15 kW IWM as research object to quantitatively analyze the temperature distribution of rated and peak conditions of the motor under different eccentricities. The influence law of eccentricity on the thermal characteristics of IWM is obtained. Results show that the eccentricity of motor has substantial influence on the temperature distribution of stator and rotor.