This study employed the Entropy-TOPSIS comprehensive evaluation method to construct an evaluation indicator system encompassing three dimensions—healthcare resource input, healthcare service efficiency, and healthcare service output—and used it to evaluate the service capacity of primary healthcare institutions in the Yangtze River Delta from 2020 to 2024. The results showed that the gaps in comprehensive scores of primary healthcare service capacity across the region narrowed year by year. Jiangsu Province ranked first, with its score rising with fluctuations from 0.512 in 2020 to 0.516 in 2024; Anhui and Zhejiang provinces also demonstrated upward trends, whereas Shanghai’s score declined from 0.511 in 2020 to 0.484 in 2024. Overall, the service capacity of primary healthcare institutions in the Yangtze River Delta improved with fluctuations, yet issues such as imperfect inter-regional coordination mechanisms persist. Future efforts should focus on establishing collaborative development mechanisms for primary healthcare, building regional health information sharing platforms, and improving joint prevention and control mechanisms for public health emergencies, thereby promoting the rational allocation of primary healthcare resources and enhancing health service capacity throughout the region.