In a motor control system, the parameters tuning of speed and position controller depend on the value of the moment of inertia. A new moment of inertia identification scheme for permanent magnet motor system was proposed in this paper. This is an extension of the existing acceleration deceleration methods, which solves the large moment of inertia identification error caused by variable angular acceleration, large calculation error of inertia torque, and large measurement noise in the acceleration process. Based on the fact that the angular acceleration is not constant and the sampling signal is noisy, the integral chain differentiator was used to calculate the instantaneous angular acceleration at any time and suppress the sampling signal noise at the same time. The error function with instantaneous angular acceleration and inertia torque as parameters was designed to estimate the moment of inertia. In order to calculate the inertia torque accurately, viscous friction torque was considered in the calculation of inertia torque, and Kalman filter was used to estimate the total load torque to solve the problem of under rank of motor motion equation. Simulation and experimental results showed that the proposed method could effectively identify the moment of inertia in both noisy and noiseless environments.