Urbanization leads to dramatic changes in habitat quality, which significantly affects population health. Research on the coupling coordination relationship between new urbanization and health production efficiency is conducive to improving residents' well-being and urban sustainable development. In this article, we adopted the super-efficient SBM model and entropy value method separately to evaluate the spatiotemporal variation characteristics of health production efficiency and new urbanization in China. Then, we used the coupling coordination degree model to investigate the interactive coercing relationship between new urbanization and health production efficiency. Finally, the panel Tobit model is used to analyze the factors influencing the coupled coordination of the two systems. The results showed that the new urbanization levels of 31 provinces in China have all steadily increased from 2003 to 2018. Health production efficiency exhibited a fluctuating but increasing trend, and its regional differences are gradually narrowing. Health production efficiency and new urbanization have developed in a more coordinated direction, with a spatial pattern of "high in the southeast and low in the northwest." Meanwhile, the relative development characteristics between the two systems have constantly changed, from the new urbanization lagged type to the two systems synchronized type and the health production efficiency lagged type. Population density, economic development level, government financial investment, and government health investment positively impact the coupling coordination degree of the two systems. In comparison, individual health investment harms the harmonization of the two systems.