Access of series reactor greatly restrains the short circuit current of power system. At the same time, it brings some negative effects to the relay protection of power system. In this paper, electromagnetic transient simulation software PSCAD/EMTDC is used to simulate the influence of series reactor in normal state and fault state on relay protection. And the mechanism of its influence on relay protection is analyzed and found out. On this basis, the relay protection setting scheme based on the different installation position of series reactor is proposed, and different setting principles in the setting scheme of the same installation position are put forward further. Through the comparison and analysis of the advantages and disadvantages of different principles of setting schemes, the optimal setting principle which can minimize the influence of series reactor on relay protection is found out, which provides theoretical basis for the later engineering application. This work is supported by National Natural Science Foundation of China (No.51467019).