Agricultural and industrial production activities generate GDP and greatly improve the quality of life of residents. At the same time, these activities also lead to increased energy consumption and emit large amounts of pollutants, which affect public health. However, there has been little past research focused on all the above associations. This study innovatively proposes a parallel two-stage EBM-DEA model to re-measure health production efficiency. The objective is to conduct a joint analysis of the economic development, pollutant emissions and human health of agriculture and industry in 30 provinces in China from 2016 to 2020, and calculate the health production efficiency, stage efficiency (agricultural production efficiency, industrial production efficiency and health efficiency) and environmental pollution efficiency. The research shows that the health production efficiency in other provinces has not reached the efficiency frontier except in Beijing, Fujian, Zhejiang, and Ningxia. In addition, there is room for improvement to varying degrees. In terms of geographical disparity, agricultural production efficiency and health efficiency are distributed in the trend of east > west > central, whereas industrial production efficiency is distributed in a ladder shape from east > central > west. Health efficiency contributes to overall efficiency, whereas agricultural and industrial production efficiencies drag down overall efficiency. The discharge efficiency of various pollutants shows that China’s environmental control policies have achieved good results, but environmental problems in some provinces are still serious. Moreover, areas with higher pollutant discharge efficiency values have higher tuberculosis incidence efficiency values. Furthermore, provinces should pay attention to improving the efficiency of medical and health fund utilization.