The optimal identification algorithm of fuzzy systems is presented for rule-based fuzzy modeling of nonlinear complex systems. Nonlinear systems are expressed using the identification of structure such as input variables and fuzzy input subspaces, and parameters of a fuzzy model. In this paper, the rule-based fuzzy modeling implements system structure and parameter identification using the fuzzy inference methods and hybrid structure combined with two types of optimization theories for nonlinear systems. Two types of inference methods of a fuzzy model are the simplified inference and linear inference. The proposed hybrid optimal identification algorithm is carried out using both a genetic algorithm and the improved complex method. Here, a genetic algorithm is utilized for determining initial parameters of membership function of premise fuzzy rules, and the improved complex method which is a powerful auto-tuning algorithm is carried out to obtain fine parameters of membership function. Accordingly, in order to optimize fuzzy model, we use the optimal algorithm with a hybrid type for the identification of premise parameters and standard least square method for the identification of consequence parameters of a fuzzy model. Also, an aggregate performance index with weighting factor is proposed to achieve a balance between performance results of fuzzy model produced for the training and testing data. Two numerical examples are used to evaluate the performance of the proposed model.