Based on panel data from 41 cities in the Yangtze River Delta from 2014 to 2023, this study employs a two-stage network Data Envelopment Analysis (DEA) model and the entropy weight method to measure the overall efficiency of healthcare 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, firstly the overall efficiency of healthcare services in the Yangtze River Delta exhibits a fluctuating downward trend, with significant regional disparities. The level of digital economy development has increased by nearly 60%, with cities maintaining the lead, yet a notable digital divide persists. Second, the digital economy significantly improves the overall efficiency of healthcare services (coefficient=0.328, P<0.01), and this finding remains robust across various tests. Third, high-quality economic development plays a partial mediating role. Lastly, the impact demonstrates dynamic persistence, with significantly positive coefficients for lags one to three periods, as well as urban heterogeneity, with central cities benefiting more. These findings provide theoretical support and decision-making references for formulating differentiated digital healthcare strategies and promoting the overall efficiency of healthcare service resources.