The investigation on vertical distribution of phytoplankton and physical-chemical characteristics was conducted in the lacustrine zone during summer stratification in Xin'anjiang Reservoir(Lake Qiandao). The Water-PAM Chlorophyll Fluorometer was used to obtain vertical profiles of phytoplankton photosynthesis. The results showed that depth of thermocline appeared between 10-20 m. Besides, the vertical profiles of pH, dissolved oxygen and turbidity were in agreement with chlorophyll-a. In summer, the phytoplankton was dominated by Bacillariophyta, C. meneghiniana was dominant in surface layer, while F. crotonensis was absolutely dominant below the surface layer. High-density of phytoplankton was found around 5-10 m below the water surface. However, a sharp decline was observed for phytoplankton density below thermocline layer. Therefore, the thermal stratification might affect the vertical distribution of phytoplankton population. Phytoplankton maximum photosynthetic efficiency had a negative relationship with water depth and the actual maximum value of photosynthetic efficiency was determined at 10 m depth.