This paper proposes a system identification method for estimating virtualised software system dynamics within the framework of a Hammerstein–Wiener model. Building on the authors’ previous work in identification and control of the software systems, the approach utilises frequency sampling filter structure to describe the linear dynamics and B-spline curve functions for the inverse static output nonlinearity. Furthermore, the issue on parameter selection for B-spline model approximation of scatter data is addressed by using a data clustering method. An experimental test-bed of virtualised software system is established to generate real observational data which are used to confirm the performance of the proposed approach. The identification results have shown that the model efficacy is increased with the proposed approach because the dimension of the nonlinear model can be significantly reduced while maintaining the desired accuracy.