Permanent magnet synchronous motor (PMSM) with high efficiency and power density is widely used in drive system of Electric Vehicle. D-q axis inductance of the motor is important in the design of a control system, but they are severely affected by magnetic saturation and cross-coupling in over-load situation. Traditional control technology ignores the effect of magnetic saturation and cross-coupling and therefore decreases the control accuracy of output torque. This paper calculated d-q axis inductance considering magnetic saturation and cross-coupling by finite element analysis (FEA). Based on this, the relationship between d-q axis inductance and current i was fitted. Maximum torque per ampere (MTPA) control considering magnetic saturation is designed. The modified method makes the inductance change with the motor current when calculating the reference current. By comparison, this paper proves the MTPA control considering magnetic saturation can achieve accurate control of output torque and can improve dynamic response of motor.