The discrepancy between the physical accessibility and perceived accessibility of public service facilities in coastal towns and villages of Fujian, China, was investigated in this study. Through a spatial distribution analysis of education and medical service facilities in Liushui Town and Xingchen Town, the equity and coverage levels of various facilities were evaluated based on the residents’ physical travel costs and perceptions. The results show pronounced spatial heterogeneity between the physical and perceived accessibility across different regions. Our findings suggest that, while certain areas boast a lot of physical access to facilities, the residents’ perceived access is significantly influenced by factors such as the terrain, transportation conditions, and the types of available travel tools. The findings of this study provide a scientific basis for optimizing the allocation of rural public service facilities, aiming to bridge the foundational service gap between urban and rural areas and promote the equitable development of rural living environments.