The reform of the salary distribution system for scientific researchers is an important starting point for promoting the coordinated development of education, science and technology, and talent undertakings. As an important salary means for talent incentive in the new era, the annual salary system emphasizes goal and contribution orientation, takes trust as the principle, and has characteristics such as matching rights and responsibilities, equal emphasis on incentive and restraint, facing the future, and having certain flexibility. It can change the traditional way of evaluating talents by one-sided quantification, is conducive to stimulating talent innovation vitality and attracting high-level international talents, and is of great significance for promoting the development of new quality productive forces. Scientific research institutes are an important base for talent team building and the forefront of the development of new quality productive forces, and can be used as a reform pilot for implementing the annual salary system. However, at present, the implementation of the annual salary system in scientific research institutes still faces challenges such as inconsistent concepts, the determination of annual salary level standards easily falling into the old path of traditional assessment and evaluation, policy implementation being restricted by other policies such as post and personnel, and insufficient internal reform enthusiasm of units, which is not conducive to the cultivation and development of new quality productive forces. Through summarizing the experience and practices of the PI annual salary system of the Institute of Biophysics, Beijing, and the multi-level annual salary system of the British Biotechnology and Biological Sciences Research Council (BBSRC), it is found that the implementation of the annual salary system in scientific research institutes generally establishes a scientific research evaluation and assessment mechanism that can fluctuate up and down in line with the characteristics of scientific research. At the same time, a strict selection mechanism is formulated for talents eligible for the annual salary system, providing an important reference for the implementation of the annual salary system in scientific research institutes in China in the future. Based on this, this paper proposes an overall reform idea of combining overall promotion with local pilots, macro coordination with micro exploration, and salary reform with scientific research evaluation. And from promoting the establishment of a scientific talent concept and modern salary concept, clarifying the elements of the annual salary system, and accelerating the construction of an annual salary system, it puts forward the reform path for scientific research institutes to implement the annual salary system, to provide policy references for the income distribution reform of scientific research institutes in China in the new era. Specifically, first, it is necessary to promote scientific research institutes to further emancipate their minds and clearly establish the ideological concept that talents are the first strategic resource and innovation is the first driving force for development. Second, it is necessary to clarify the scope of application of the annual salary system and promote the establishment of a scientific and comparable mechanism for determining the annual salary. Third, it is necessary to strengthen multi-departmental coordination, clarify specific opinions and implementation paths for promoting the implementation of the annual salary system in scientific research institutes from aspects such as overall thinking, goal principles, and specific measures. At the same time, a negative list mechanism and integrity restraint system, and a talent selection system should be established.