Abstract: Under the background of China’s protected area system reform, the optimization and integration of protected areas have already become a research hotspot. The conservation objectives of existing protected areas mainly focus on in-situ biodiversity conservation, and rarely pay attention to ecosystem services. It is conductive to improving the comprehensive benefits of protected areas to incorporate ecosystem services into the conservation objective thereof. Taking Fuzhou City in the lower reaches of Minjiang River Basin as an example, this research conducts ecosystem services assessment and gap analysis based on the equivalent factor approach and relevant value clustering tools. It proposes strategies for optimizing the protected area system in Fuzhou City from the three aspects of classification system, spatial pattern and management system. Research results show that: 1) the total ecosystem services value of Fuzhou City was 54.27 billion yuan in 2018, and the values of different types of ecosystem services in Fuzhou City are compared as follows: regulating service > supporting service > supplying service > cultural service; 2) the distribution of ecosystem service value in Fuzhou City presents a general pattern of lower in the center while higher around; 3) there are three conservation gaps in Fuzhou’s protected area system. The research proposes differential optimization strategies for conservation gap areas in different types of ecosystem services, in hope of providing a referential case for rapid assessment and optimization of municipal protected area system.