The study was based on the rice-crab culture of integrated system to analyze phytoplankton and environmental factors at the water inlet, middle and outlet of paddies in the village of Helan, Ningxia. The rice species was Qiuyou 88, and the crab variety was Eriocheir sinensis. In the experiment, four paddies (paddy 3, 6, 7 and 10) were irrigated with fish pond tail water (experimental group) and one paddy (paddy 8) was irrigated with water from Yellow River (control group).The results showed that A total of 235 phytoplankton species were identified from 8 phyla throughout four periods in experiment group,among which 153 species from 8 phyla in paddy 3, 147 species from 8 phyla in paddy 6, 143 species from 7 phyla in paddy 7 and 159 species from 8 phyla in paddy 10. A total of 127 species from 7 phyla were identified in the control group. The average density of the experimental group was higher than that of the control group (P<0.05); A total of 13 dominant species were found in the experimental group and 9 dominant species were found in the control group, all of which were dominated by Cyanobacteria. The diversity index of paddy irrigated fish pond tail water was higher than that irrigated Yellow River water, which indicated that the phytoplankton community structure of the paddy irrigated fish pond was more perfect and stable. There was no significant difference in total alkalinity and salinity between the experimental group and the control group (P>0.05), but there was significant difference in transparency, water temperature, phosphate, pH,dissolved oxygen, nitrite and ammonia nitrogen between the experimental group and the control group (P<0.05).The RDA analysis showed that pH, transparency(SD)and water temperature(WT)were identified as the main factors affecting the changes in phytoplankton community.