Background: Despite the growing literature on the efficiency and productivity of the Chinese healthcare system, less attention has been given to examining the undesirable outputs linked to healthcare services, including environmental pollution. Taking the atmospheric environmental pollution resulting from the incineration of medical waste as an undesirable output of the healthcare system, this study analyzed the growth and decomposition of Total Factor Productivity (TFP) of healthcare services across 31 Chinese provinces during the period 2005-2016. Methods: The Meta-frontier undesirable super-efficiency slack-based measure (SBM) model and the Global Malmquist-Luenberger (GML) Index were employed to analyze the growth and decomposition of TFP using the Max DEA software. Results: The results revealed that the years 2009 and 2015 marked significant changes in TFP of healthcare services in Chinese provinces. During the study period, the rate of technological change (TC) slowly declined, whereas the rate of efficiency change (EC) steadily increased. With the national average being the benchmark, the results indicated that: the TFP of 17 provinces and cities exceeded the average, the EC changes of 16 provinces and cities exceeded the average, the TC changes of 9 provinces and cities exceeded the average, and the in the Technology Gap Ratio (TGR) changes of 13 provinces and cities were above the national average. Conclusions: (1) The TFP of the healthcare services across China continued to decline slowly during the study period. (2) The effect of technical catch-up in the eastern, central, and western regions of China was significant across the three regions, whereas the effect of technical innovation was negative. (3) The TFP varied considerably among the Chinese provinces. These findings suggest that, under existing environmental constraints, relevant government departments should improve technical innovation in the supply of healthcare services and medical waste treatment, increase technical efficiency in the factor of healthcare production, strengthen regional health planning, and balance the development of regional healthcare.