The smooth online setting of relay protection in a complex loop network depends on the fast calculation of the minimal break point set. However, the existing algorithm for this set has some shortcomings in algorithm complexity, dimension of breakpoint set and computational efficiency. An algorithm to calculate the minimal break point set for relay protection online setting is proposed. Based on the inherent relationship between basic cut set matrix and basic loop matrix in graph theory, the problem of finding the break point set of a complex loop network is transformed into that of finding the break point set of basic loop based on basic cut set matrix. The minimal break point set of the network is obtained by adjusting the basic cut set matrix dynamically. Example analysis shows that the proposed algorithm can obtain the minimal break point set of the network in an effective time, and this greatly reduces the complexity of the problem. This work is supported by the National Key Research and Development Program of China (No. 2016YFB0900100).