In order to apply an engine intake air system model to engine control, it is necessary to calculate the intake air system model quickly and accurately under constraints of computational performance. Therefore, a study has been made on a method for calculating the intake air system model implemented by an analog LSI at short times. However, the problem is to include the model error in the intake air system model based on the analog LSI of present state. This paper reports a compensation of the intake air system model with error by Extended Kalman Filter (EKF).A basic model that reproduces model errors of analog LSI model is built, and a compensator based on EKF is designed. As a result, it is confirmed that the compensator reduces the model errors by half. Moreover, this paper reports the numeric solution in order to reduce the hunting phenomenon of the engine intake air system model.