The medical service system of Traditional Chinese Medicine（TCM） is an important shield to maintain the national health. Improving the TCM medical service system is the primary task of the development of TCM. Only the indices are determined， can TCM medical services be developed properly. This paper aims to construct the comprehensive evaluation index of TCM medical service system in China by exploratory factor analysis. The study found that the comprehensive evaluation of TCM medical service system could be divided into 3 primary indicators and 14 secondary indicators. The development of TCM medical service system in China was unbalanced and inadequate， showing the trend of that East was strong and West was weak， South was strong and North was weak. North China and East China were generally superior to Northwest and Southwest China in terms of revenue and expenditure of TCM medical services. The per capita of medical resources in Southwest and Northwest were stronger than those in Central and South China， but the overall medical resources were weaker than those in East China and North China. TCM medical service institutions in East China， South China and Central China had achieved better service effects and higher economic benefits with less resources input， which further indicated the efficient allocation of resources and the balanced operation of TCM medical service institutions.