Evolutionary design related to the optimal design of Polynomial Neural Networks (PNNs) structure for model identification of complex and nonlinear system is studied in this paper. The PNN structure is consisted of layers and nodes like conventional neural networks but is not fixed and can be changable according to the system environments. three types of polynomials such as linear, quadratic, and modified quadratic is used in each node that is connected with various kinds of multi-variable inputs. Inputs and order of polynomials in each node are very important element for the performance of model. In most cases these factors are decided by the background information and trial and error of designer. For the high reliability and good performance of the PNN, the factors must be decided according to a logical and systematic way. In the paper evolutionary algorithm is applied to choose the optimal input variables and order. Evolutionary (genetic) algorithm is a random search optimization technique. The evolved PNN with optimally chosen input variables and order is not fixed in advance but becomes fully optimized automatically during the identification process. Gas furnace and pH neutralization processes are used in conventional PNN version are modeled. It shows that the designed PNN architecture with evolutionary structure optimization can produce the model with higher accuracy than previous PNN and other works.