The invention relates to a method for optimizing and controlling operation of membrane bioreactor based on mechanism model, relating to the sewage treatment system process target control field. The invention solves the problem that self optimization control of the existing membrane bioreactor based on experience is lack of effective control, no-noise signal is input to a DPS model to obtain a predicted optimization path of control variable and control target; noise-containing signal is input to a NMPC model, and meanwhile input quantity set u and output quantity set y are obtained combining the predicted optimization path, input parameter is selected from the input quantity set u and is input to a basic control BC module, actual input parameter ubc is obtained, when the output target under the actual input parameter ubc accords with preset target y, the input parameter is selected as operation parameter of the membrane bioreactor, and optimization and control on operation of the membrane bioreactor is completed. The invention is applicable to effective control of sewage treatment system.