BackgroundThe hierarchical medical system (HMS) refers to the classification of treatment according to disease priorities based on severity and difficulty to promote the fairness of medical services for residents, which is regarded as the key to the success of medical reform in China.MethodsIn the past decade of “New Medical Reform,” the efficiency of HMS, including secondary and tertiary hospitals and primary healthcare centers (PHCs), was measured horizontally and vertically by employing the combination of an output-oriented superefficiency slack-based model-data envelopment analysis (SE-SBM-DEA) model with the Malmquist total factor productivity index (MTFP). In the second stage, the overall technical efficiency (OTE) scores were regressed against a set of environmental characteristics and several managerial factors through bootstrapping truncated regression.ResultsOn average, the OTE score in tertiary hospitals was 0.93, which was higher than that in secondary hospitals and PHCs (0.9 and 0.92, respectively). In terms of trend, the OTE of tertiary hospitals declined at first and then increased. The opposite was true of secondary hospitals, in which the APC of the OTE was 10.82 and −3.11% in early and late 2012, respectively. The PHCs generally showed a fluctuating downward trend. In the aspects of productivity, all institutions showed a downturn by an annual average rate of 2.73, 0.51, and 2.70%, respectively. There was a significant negative relationship between the ratio of outpatients to inpatients and tertiary hospitals. Additionally, the medical technical personnel per 1,000 population negatively affected PHCs. In contrast, the GDP per capita had a significantly positive effect on tertiary hospitals, and the number of beds per 1,000 population positively influenced PHCs.ConclusionThe efficiency of medical institutions at various levels in HMS was unbalanced and took the form of an “inverted pyramid.” Multilateral factors influence the efficiency of HMS, and to address it, multi-intervention packages focusing on sinking high-quality medical resources and improving healthcare capacity, and guiding hierarchical medical practice should be adopted.