Objective To explore the impact of policy instruments and innovation on the informatization of rural health service system. Methods Central government policy documents related to the informatization of rural health service system, publicly released between 2009 and 2023, were collected using web crawler tools. Keyword extraction was conducted through word frequency analysis and term frequency-inverse document frequency (TF-IDF) calculation. Content analysis of policy texts was carried out from the dual perspectives of policy instruments and the policy innovation process. An exponential growth model was used to fit the evolutionary trend. Results Among the 45 central policies included, policy instruments were used 178 times in total. The demand-side policy instruments accounted for the highest proportion (71 times, 39.89%), reflecting policy responsiveness to the diversified needs of rural healthcare services. The supply side policy instruments have been used a total of 51 times, with the “information system and infrastructure construction” policy instrument being the most frequently (33 times), indicating a national focus on enhancing investment in digital infrastructure and technology. In terms of the policy innovation process, policy instruments were primarily utilized during the adoption stage of policy ideas (55.06%), followed by the implementation stage (38.20%), with the initiation stage being the least influenced (6.74%). The initiation stage was relatively evenly influenced by all 3 types of policy instruments; the adoption stage was mainly influenced by demand-side instruments, while the implementation stage was dominated by supply-side instruments. This trend reflected a policy shift in recent years from value guidance toward practical operability and implementation, demonstrating alignment with the real-world needs of advancing digital technology and improving governance capacity. Conclusion Different policy instruments exhibit stage-specific effectiveness in driving informatization innovation, indicating the need to precisely align instruments with each phase of the policy innovation process to advance informatization in a targeted manner. Top-level policy documents should be refined to clearly define relevant policy concepts. Additionally, execution pathways must be detailed to accelerate infrastructure development in remote and economically disadvantaged regions.