For the disadvantage of traditional production mode, an operation optimization model is put forward on the basis of analyzing workshop production system operation. The Features of the model are real-time, dynamic, multi-objective and multistage. The algorithm called ‘Harmonizing Cluster Results’ for the model is presented in order to solve the difficulties of solution for the workshop production system operation model. Then the model is simplified into some submodels, such as production ability optimization submodel, time optimization submodel, balancing and harmonizing submodel etc. Finally the operation optimization model and its solution algorithm are applied to an assembly line of energy meter in a factory. With the help of ‘Witness’ the application case simulation results showed that the model is accurate and its solution algorithm is reasonable and available.