This article examines the health system performance impact of China’s new round of healthcare reform adopted in 2009. Specifically, we evaluated productivity and efficiency of health production pre- and post-reform period, compared the effects across all the 31 provinces of mainland China and identified potential determinants. As a major source of disability and premature mortality in China, non-communicable diseases (NCDs) had been the focus of our analysis, and the period during 2008–2015 was considered to allow enough time for the policy to have meaningful impact on the country’s health system. Productivity and efficiency performance were analyzed using a bootstrapping data envelopment analysis (DEA) and the Malmquist productivity index (MPI) techniques, while a Tobit regression technique was used to identify determinants of inefficiency. We find that after the reform efficiency and productivity had declined across large number of provinces. Mean overall technical efficiency (OTE) post 2009 was about 30% lower than the potential maximum capacity, while productivity also fell at a rate of 7.57% per annum. Trends in productivity and efficiency performance were largely linked to patterns of scale of technological change observed during the study period. The findings suggest that efficiency and productivity can be improved through enhancing financial security, optimizing health resource allocation, particularly between human resources for health and hospital beds, and expanding cost-effective technology within the health sector. Better urban planning practices and investment in education were also found to contribute to improved efficiency of NCDs services.