Background <p>China’s healthcare reform has shifted its focus toward enhancing quality and systemic efficiency, yet significant regional disparities persist. Guangdong Province offers a critical case for examining health service efficiency inequalities due to its pronounced internal development gap between the Pearl River Delta (PRD) and the Eastern, Western, and Northern regions.</p> Objective <p>The objective of this study is to systematically evaluate the efficiency of the health service system in Guangdong Province from 2015 to 2024. The study will identify regional disparities and isolate the impact of external environmental factors in order to reveal performance after adjusting for observed environmental factors and statistical noise.</p> Methods <p>A three-stage Data Envelopment Analysis (DEA) model was employed to assess the efficiency of 21 prefecture-level cities in Guangdong. The input-oriented BCC model was utilized in the initial stage to obtain preliminary efficiency scores. In the second stage, Stochastic Frontier Analysis (SFA) was employed to adjust input slacks for environmental variables (GDP per capita and population density). The third stage of the process involved a re-evaluation of efficiency, with the inputs being adjusted accordingly. The input variables encompassed medical technical personnel, hospital beds, and medical institutions; the output variables comprised outpatient visits, inpatient cases, average length of stay, and bed utilization rate. A Malmquist Productivity Index analysis was also conducted to capture dynamic productivity changes over the study period.</p> Results <p>The initial DEA revealed an average technical efficiency (TE) of 0.929. Following adjustment, the mean TE increased to 0.932, indicating a slight underestimation due to unfavorable environmental factors. Scale efficiency (SE, mean = 0.986) was consistently higher than pure technical efficiency (PTE, mean = 0.946). After adjusting for observed environmental factors, the PTE estimates, which served as composite indicators of operational performance, suggested that dimensions related to management and technology represented the primary bottleneck. Significant regional disparities were confirmed, with the PRD region demonstrating superior and more resilient efficiency (adjusted TE = 0.948) compared to Eastern (0.902), Western (0.924), and Northern (0.933) Guangdong. And the period following the onset of the SARS-CoV-2 pandemic coincided with a notable decline in PTE after 2019, highlighting systemic vulnerabilities. Malmquist analysis revealed that total factor productivity declined by 2.5% annually over the decade, associated primarily with technological regression (TC = 0.972) rather than efficiency losses. Productivity dropped by17.7% in 2019–2020, temporally aligned with the pandemic’s onset, though sustained recovery occurred after 2022 with TFP reaching 1.047 in 2022–2023 and 1.042 in 2023–2024. Considerable heterogeneity existed across cities, with Dongguan achieving positive TFP growth (1.003) while most others experienced declines.</p> Conclusion <p>The health service system of Guangdong has achieved a relatively balanced scale of resource allocation. However, it encounters challenges with regard to managerial and technical performance. It is recommended that policy interventions shift focus from quantitative expansion to the enhancement of intrinsic operational capabilities, particularly in Eastern, Western, and Northern Guangdong, while also prioritizing technological innovation to address the systemic technological regression identified in this study.</p>