In order to understand the carbon sequestration of phytoplankton in freshwater aquaculture ponds of Litopenaeus vannamei and to find out the relationship among water quality， phytoplankton and carbon sequestration， the primary productivity of the water of Litopenaeus vannamei aquaculture ponds in Fengxian District， Shanghai was detected by black and white bottle method， and the carbon sequestration of phytoplankton was estimated. The results showed that a total of 45 genera belonging to 7 phylum of phytoplankton were observed in the three ponds， including 19， 8， 11， 3， 2， 1 and 1 genera of Chlorophyta， Cyanophyta， Bacillariophyta， Euglenophyta， Chrysophyta， Dinophyta and Cryptophyta， respectively. The phytoplankton densities in pond Ⅰ， Ⅱ and Ⅲ were （7.99±7.84）×10⁵， （1.86±1.55）×10⁶ and （2.57±1.66）×10⁶ ind/L， respectively. There were four species of common dominance in the three ponds， namely Scenedesmus， Oscillatoria， Navicula and Cyclotella. The variation range of daily carbon sequestration per unit area （D_CS） of phytoplankton was 0.27-4.92 g C/（m²·d）， the average value was （1.62±1.12） g C/（m²·d）， the cumulative carbon sequestration of phytoplankton increased slowly with the extension of the cultivation time during the whole cultivation period， and the cumulative carbon sequestration of the 3 experimental ponds was 0.80， 1.11 and 1.31 t C at the end of aquaculture. The results of multiple stepwise regression analysis showed that Chlorophylla （Chl.a）， Total Nitrogen （TN）， Temperature （T）， pH， phytoplankton Euglenophyta and Cyanophyta were the main environmental factors affecting the D_CS of phytoplankton. Pearson correlation analysis and redundancy analysis showed that Chl.a， TN， T， Euglenophyta and Cyanophyta were the key factors affecting the carbon sequestration of phytoplankton， and these results were helpful for us to understand the effects of water quality and phytoplankton community on the carbon sequestration of phytoplankton in Litopenaeus vannamei fresh water aquaculture ponds.