Based on the systemic investigation on the feedforword neural network, for the problem of the structure design of the RBF neural network, a new flexible structure design method is used for RBF neural network in this paper. By computing the output-information (OI) of the hidden neurons and the multi-information (MI) of the hidden nodes and output nodes, the hidden nodes in the RBF neural network can be inserted or pruned, thus the topology of the network can be modulated. This method can effectively solve the structure design of the RBF neural network. The grad-descent method for the parameter adjusting ensures the exactitude of the flexible RBF neural network (F-RBF). The structure of the RBF neural network is self-organizing, and the parameters are self-adaptive. In the end, the proposed F-RBF is used for approximating the classical non-linear functions and modelling key parameters of the wastewater treatment process. The results show that the F-RBF obtains a favorable dynamic character response and the approximating ability. Especially, comparied with the minimal resource allocation networks (MRAN), the generalized growing and pruning RBF (GGAP-RBF) and the self-organizing RBF (SORBF), the proposed algorithm is more effective in terms of training time, generalization, and neural network structure.