Scientific research institutes are an important force for comprehensively implementing my country’s innovation-driven development strategy and building a world power in science and technology. The salary system of scientific research institutes is an important support for achieving the above goals. In order to make the salary system of scientific research institutes more in line with the characteristics of scientific research institutes，it is necessary to further reform and improve the salary system of scientific research institutes. The specific path is that further clarify the government’s management responsibilities and boundaries for the salary management of public scientific research institutions，and adopt a more flexible distribution method，apply the total compensation theory to enrich the compensation system of scientific research institutes，establish and improve the salary level determination and growth mechanism，establish a total salary management model that combines budget management，self-discipline and supervision, and further clarify the projects that are not limited by the total salary (or performance salary)，and promote the formation of a fair and effective internal distribution mechanism in scientific research institutions，pay attention to the “last mile” problem of the implementation of salary incentive policies，and strengthen the government’s investment responsibility and ensure the stability of the source of salary funds.