A cross-layer secure communication scheme for multiple input multiple output (MIMO) system based on spatial modulation (SM) is proposed in this paper. The proposed scheme combined the upper layer stream cipher with the distorted signal design of the MIMO spatial modulation system in the physical layer to realize the security information transmission, which is called cross-layer secure communication system. Simulation results indicate that the novel scheme not only further ensure the legitimate user an ideal reception demodulation performance as the original system, but also make the eavesdropper' error rate stable at 0.5. The novel system do not suffer from a significant increasing complexity.