Model predictive control (MPC) methods are widely used in the power electronic control field, including finite control set model predictive control (FCS-MPC) and continuous control set model predictive control (CCS-MPC). The degree of parameter uncertainty influence on the two methods is the key to evaluate the feasibility of the two methods in power electronic application. This paper proposes a research method to analyze FCS-MPC and CCS-MPC’s influence on the current prediction error of three-phase active power filter (APF) under parameter uncertainty. It compares the performance of the two model predictive control methods under parameters uncertainty. In each sampling period of the prediction algorithm, different prediction error conditions will be produced when FCS-MPC cycles the candidate vectors. Different pulse width modulation (PWM) results will be produced when CCS-MPC solves the quadratic programming (QP) problem. This paper presents the simulation results and discusses the influence of inaccurate modeling of load resistance and inductance parameters on the control performance of the two MPC algorithms, the influence of reference value and state value on prediction error is also compared. The prediction error caused by resistance mismatch is lower than that caused by inductance mismatch, more errors are caused by underestimating inductance values than by overestimating inductance values. The CCS-MPC has a better control effect and dynamic performance in parameter mismatch, and the influence of parameter mismatch is relatively tiny.