To reduce thermal damage to maize quality caused by microwave sterilization, firstly 13 parameters of seed quality and processing quality of maize were determined, secondly the data matrix was converted by the method of subordinate function, and then the comprehensive evaluation of the quality of maize was performed by factor analysis. On this basis, the optimal parameters of mould inactivation by microwave processing were selected. The results indicated that, the method of subordinate function could integrate the positive and negative characteristics in the synthetical evaluation, so the matrix converted with this method was suitable for factor analysis. Four factors affecting quality evaluation of maize were extracted and their cumulative variance was 94.45%, which were physiological and biochemical characteristics factor, viscosity property factor, content and composition of starch factor and pasting property factor in sequence. The synthetical quality evaluation of maize suggested that，maize quality changes resulted from the interaction of the initial moisture content of maize, microwave processing temperature and processing time. Therefore, microwave processing parameters, namely, 70℃(14 min), 50℃(22min) and 60℃(18 min) should be respectively adopted when the initial moisture content of maize were 13.8%, 18.4% and 22.6%.