Accurate models play important roles in capturing the salient characteristics of the network traffic, analyzing and simulating for the network dynamic, and improving the predictive ability for system dynamics. In this study, the ensemble of the flexible neural tree (FNT) and system models expressed by the ordinary differential equations (ODEs) is proposed to further improve the accuracy of time series forecasting. Firstly, the additive tree model is introduced to represent more precisely ODEs for the network dynamics. Secondly, the structures and parameters of FNT and the additive tree model are optimized based on the Genetic Programming (GP) and the Particle Swarm Optimization algorithm (PSO). Finally, the expected level of performance is verified by using the proposed method, which provides a reliable forecast model for small-time scale network traffic. Experimental results reveal that the proposed method is able to estimate the small-time scale network traffic measurement data with decent accuracy.