Against the backdrop of the deep advancement of the Digital Yangtze River Delta initiative and the Healthy China strategy, exploring the impact of the digital economy on the overall efficiency of medical service resources holds significant theoretical and practical implications. Based on panel data from 41 cities in the Yangtze River Delta from 2014 to 2023, this study employs a two-stage network DEA model and the entropy weight method to measure the overall efficiency of medical service resources and the comprehensive index of digital economy development, respectively. Panel regression and mediation effect models are used to empirically analyze the impact and its underlying mechanisms. The results indicate that: ① The overall efficiency of medical services in the Yangtze River Delta exhibits a fluctuating upward trend with significant regional disparities; the level of digital economy development has nearly tripled, with leading cities outperforming others, yet a notable "digital divide" persists. ② The digital economy significantly improves the overall efficiency of medical services (coefficient = 0.328, P < 0.01), and this finding remains robust under various tests. ③ High-quality economic development plays a partial mediating role. ④ The impact demonstrates dynamic persistence (coefficients for lags one to three periods are significantly positive) and urban heterogeneity, with central cities benefiting more. These findings provide theoretical support and decision-making references for formulating differentiated digital health strategies and promoting the overall efficiency of medical service resources.