Abstract: We investigated the chlorophyll a (Chl-a) concentration in the middle South China Sea (12°N~18°N, 110°E~117°E) in July and August 2014 to provide valuable data for the study of vertical distribution of Chl-a. The results show that: 1) Chl-a in the middle South China Sea increased first and then decreased in depth. High concentration accumulated in depth of 30~70 m. 2) At subsurface layer, the maximum of Chl-a (SCM) intensity varied from 0.94 mg·m^-3to 4.69 mg·m^-3 with an average of 1.90 mg·m^-3, which was 18.10 times compared with satellite surface Chl-a. SCM depth varied from 4 m to 75.36 m. SCM thickness varied from 19.01 m to 80.36 m. 3) The upwelling had great effect on the vertical distribution of Chl-a according to the distribution characteristics in Transect A and B. Coastal upwelling in Transect A showed the greatest intensity, smallest depth and largest thickness of SCM, while Zhongsha Islands upwelling in Transect B showed the greatest intensity, smallest depth and thickness.