In order to solve the problems that multi micro-grids brings to the protection of distribution network, a fault location matrix algorithm based on master-slave regional pilot protection system is proposed. Firstly, a network matrix which is based on the information of the auxiliary machine sending and the present network structure and the operation mode is formed, and simultaneously, a fault information matrix based on fault current directional information collected by each slave protection is formed; then, a fault judgment matrix is got by the additive operation of the two matrices; finally, we can locate the fault with corresponding criterion and send order to the auxiliary machine to cut breaker isolated fault. This algorithm is simple, fast and small memory space, which can locate single or multi fault of both open-loop distribution network and close-ring distribution network. The algorithm is unaffected when the network structure is changed or the micro-grid is switched, which has a certain self-adaptive. This work is supported by National Natural Science Foundation of China (No. 51307104) and Shanghai Engineering Research Center of Green Energy Grid-connected Technology (No. 13DZ2251900).