Based on the research object of 30 provinces (municipalities and regions) in China, a comprehensive evaluation index system of water-energy-food security including 30 indices is established. The water-energy-food security in 30 provinces (municipalities and regions) from 2003 to 2019 is measured and analyzed. The results show that the overall security of water-energy-food system in 30 provinces (municipalities and regions) gradually increases from 2003 to 2019. The water-energy-food security in the provinces along the Yangtze River Economic Belt has significantly increased, exhibiting obvious spatial agglomeration characteristics. The water-energy-food security in Beijing-Tianjin-Hebei region is relatively low due to the higher demands of domestic water and ecological water, while the fluctuation of water-energy-food security in Ningxia and Xinjiang is obvious, which is mainly caused by more application of chemical fertilizer and higher disaster rate of crops. The energy security and food security vary distinctly among provinces (municipalities and regions), which reflects that resource production capacity is generally inconsistent with environmental governance capability.