Abstract: In order to explore the dynamic differences of intracellular microcystins (IMCs) and key influencing factors in spring for Lake Chaohu and Lake Taihu, samples were analyzed from different lake areas of this two lakes in March, April and May of 2019. The results indicated that IMCs showed obvious temporal and spatial distribution characteristics in Lake Chaohu and Lake Taihu during the sampling period, the concentration of IMCs increased month by month, and IMCs in the high eutrophication lake area was significantly higher than that in the low eutrophication lake area. IMC-LR was the main isomer of IMCs in the two lakes, accounting for 65.10% and 58.10%, respectively. IMCs concentration between the two lakes were significantly different, the average concentration of IMCs in Lake Chaohu (0.077, 0.238, 0.632 μg/L) was obviously higher than that in Lake Taihu (0.021, 0.031, 0.166 μg/L), and the toxicity of IMCs per unit biomass (IMCs/Chla and IMC-LR/Chla) was also significantly higher than that in Lake Taihu. The correlation analysis showed that TN, TP and TN/TP were the key environmental factors affecting the concentration of IMCs and the toxicity of IMCs per unit biomass, and the abundance and capacity of toxin-producing algae may be the important reasons for the difference.