Aiming at the existing problems of the Secure Network Encryption Protocol(SNEP) including that the protocol is too dependent on the base station, large energy consumption to calculate the key, the key distribution of low security, the network adopts the clustering structure, and introduces the matrix and the multi-key space theory to improve the SNEP. The calculation of the communication key can be carried out autonomously between the nodes using the loaded matrix information. Through the analysis, it is indicated that the program can reduce the base station dependency , prevent witch attacks, and decrease the calculation of the base station and storage requirements, also the node computing and storage overhead are not increased significantly; the network is of high security, and better scalability.