A novel 3D surface generation modelling method for micro milling which considers the effect of machining nonlinear dynamics is proposed based on homogeneous matrix transformation. Considering the effects of machining process kinematics, tool run-out and the nonlinear dynamic regenerative effect of the machining system, the relationship between machining process and surface topography is established. On this basis, three typical machining cases, namely static stable, dynamic stable and unstable machining, are investigated in this paper. The machining experiment results demonstrate that the proposed surface generation model can accurately predict surface topography generation and roughness values with different machining conditions. Thus, it can be used not only to optimize the machining parameters for improving the micro-milled surface quality but also to predict the surface topography under pre-defined machining parameters.