In this paper, we introduce a new architecture of PSO-based Polynomial Neural Networks (PNN) and discuss its comprehensive design methodology. The conventional PNN is based on a extended Group Method of Data Handling (GMDH) method, and utilized the polynomial order (viz. linear, quadratic, and modified quadratic) as well as the number of node inputs fixed (selected in advance by designer) at Polynomial Neurons located in each layer through a growth process of the network. Moreover it does not guarantee that the conventional PNN generated through learning results in the optimal network architecture. The PSO-based PNN results in a structurally optimized structure and comes with a higher level of flexibility that the one encountered in the conventional PNN. The PSO-based design procedure being applied at each layer of PNN leads to the selection of preferred PNs with specific local characteristics (such as the number of input variables, input variables, and the order of the polynomial) available within the PNN. In the sequel, two general optimization mechanisms of the PSO-based PNN are explored: the structural optimization is realized via PSO whereas in case of the parametric optimization we proceed with a standard least square method-based learning. To evaluate the performance of the PSO-based PNN, the model is experimented with using Gas furnace process data, and pH neutralization process data. For the characteristic analysis of the given entire data with non-linearity and the construction of efficient model, the given entire system data is partitioned into two type such as Division I(Training dataset and Testing dataset) and Division II(Training dataset, Validation dataset, and Testing dataset). A comparative analysis shows that the proposed PSO-based PNN is model with higher accuracy as well as more superb predictive capability than other intelligent models presented previously.