Harmful cyanobacterial blooms are increasing in frequency and severity, which makes their toxic secondary metabolites of microcystins (MCs) have been widely studied, especially in their distribution and influence factors in different habitats. However, the distribution of MCs on the early growth stage of harmful cyanobacteria and its influence factors and risks are still largely unknown. Thus, in the present study, two reservoirs (Lutian Reservoir and Lake Haitang) with different trophic status in China have been studied weekly from March to May in 2018, when the cyanobacteria communities were just in the early growth stage, to investigate the variation of MCs concentration and the relationships between MCs and environmental parameters. During the investigation, Lutian Reservoir and Lake Haitang were found to be mesotrophic and light eutrophic, respectively. In Lutian Reservoir, the concentration of EMCs (extracellular MCs) was obviously higher than that of IMCs (intracellular MCs) with a mean value of 0.323 and 0.264μg/L, respectively. Meanwhile, the concentration of EMCs also fluctuated more sharply than that of IMCs. Congeners of IMC-YR and EMC-LR were respectively dominant in total concentrations of IMCs and EMCs. Unsurprisingly, in Lake Haitang, the concentrations of IMC and EMC were both significantly higher than that in Lutian Reservoir with a mean concentration of 0.482 and 0.472μg/L, respectively. Differently, the concentration of MC-YR was dominant in both IMCs and EMCs, followed by MC-LR. In correlation analysis, the IMCs were significantly and positively correlated with the density and biomass of phytoplankton phyla and potential MCs-producing cyanobacteria and the parameters of water temperature (WT), nutrients, and organic matters. Similar results were also observed for EMCs. While the different variations of MCs in the two reservoirs might be primarily caused by the differences in WT, nutrients (especially phosphorus), organic matters, and the composition of MCs-producing cyanobacteria. In addition, the coexistence of the dominant species of Pseudoanabaena sp., which can produce a taste-and-odor compound of 2-methylisoborneol (2-MIB), might have a significant impact on the concentration and toxicity of MCs. Our results suggested that the risks posed by MCs at the early growth stage of cyanobacteria should also deserve our attention, especially in mesotrophic water bodies.