Abstract: Using Pak-Choi (Brassica campestris ssp. chinensis Makino) variety ‘Xinaiqing’ as the tested material, we investigated the effects of waterlogging with different stress depth on its photosynthetic characteristics, chlorophyll content and chlorophyll fluorescence. Results showed that: under 5 d waterlogging, net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), photosystemⅡ (Fv/Fm) of the surface submergence of soil and the semi-submergence of plants were significantly lower, accounting for 43.1% and 22.1%, 26.4% and 14.3%, 40.2% and 33.2%, and 87.9% and 77.1% of the control, respectively. Chlorophyll content, effective photochemical quantum yield (Yield) and electron transport rate (ETR) were also significantly decreased. Water use efficiency (WUE) and coefficient of photochemical quenching (qP) during root submergence were slightly lower, but significantly decreased during the semi-submergence of plants. However, intercellular carbon dioxide concentration (Ci) and non-photochemical quenching coefficient (qN) of the surface submergence of soil and the semi-submergence of plants were significantly increased, accounting for 105.3% and 115.6%, and 120.6% and 147.4% of the control, respectively. The above results indicated that there were significant effects on photosynthetic characteristics under waterlogging stress, and these parameters showed greater change under submergence waterlogging stress than that under root waterlogging stress.