In order to explore the effects of different agricultural fertilization management on the phytoplankton community, the phytoplankton community characteristic and water environmental factors were investigated in winter and summer in Daizhuang organic village and conventional farming area of Jurong, Jiangsu Province. Our results showed that the phytoplankton communities were composed of 95 and 111 species of 7 phyla in organic (OFR) and conventional farming regions (CFR) in winter, 102 species of 7 phyla and 112 species of 6 phyla in summer, respectively. The phytoplankton varied from Cryptophyta-Chlorophyta type in winter to Cyanophyta-Chlorophyta type in summer in OFR, and from Cryptophyta-Chlorophyta type to Cyanophyta-Bacillariophyta type in CFR, indicating that Cyanophyta gradually replaced the dominant position of Cryptophyta. There was no significant difference in phytoplankton alpha diversity between organic and conventional farming ponds in summer, but the phytoplankton species richness and Shannon-Wiener diversity of Cyanophyta and Euglenophyta in CFR was significantly higher than that in OFR in winter. The IndVal analysis further revealed that Nitzschia palea and Cyclotella meneghiniana were the indicative species in OFR, while Euglena acus, Ankistrodesmus acicularis, Synedra ulna and Ankistrodesmus angustus were the indicative species in CFR. These algae often occurred in meso-eutrophic waters, indicating that the concentration of nitrogen and phosphorus in water was higher. This may be closely related to the nitrogen and phosphorus runoff. Pearson correlation analysis showed that there was no significant relationship between phytoplankton alpha diversity and environmental factors in two regions, but species richness and Pielou's evenness in CFR were significantly correlated with phosphate, total nitrogen, ammonia nitrogen and pH. Mantel test showed that the community dissimilarity in OFR was only significantly affected by total nitrogen and ammonia nitrogen in winter. While in CFR, community dissimilarity was affected by the alternation of nitrogen and phosphorus nutrients in winter and summer. These findings should be useful for future efforts to recover biodiversity and optimize fertilization management.