A software for automatic parameter estimation (PEST) was used to estimate 24 parameters in the root zone water quality model (RZWQM2) and analyze the sensitivity of each parameter by controlling the proportion of function values of simulation difference from various observation variables in the objective function, including soil moisture, soil nitrate, leaf area index and yield of crop. The results show that parameters of PHW, P1VW and PHM were the three most influential parameters to the overall simulation performance of the RZWQM2 model when the proportion of simulation difference for each observation variable was closest. In contrast to the trial and error method, RZWQM2 model after calibrated with PEST could accurately simulate the moisture and nitrogen transport in soil profile and crop growth in a rotation system of waxy mazy and winter wheat. This study could help estimate RZWQM2 parameters in different agricultural management practices and could also provide a reference for the application of PEST in other models for parameter optimization.