The multiscale waterflow watershed system which were from the primary tributary to the mainstream in the Poyang Lake, and then entering into the lake area (Xiangxi River→Jiazhu River→Gangjiang River→Pangyang Lake), was selected as the study site. By monitoring the carbon and silicon transportation at multiscale in the Poyang Lake watershed, we aim to understand the relationship between the distribution of phytoplankton community and the carbon and silicon transport at multiscale in Poyang Lake. The results showed that C, Si, and C/Si ratio of the Poyang Lake watershed exhibited spatial changes. The concentrations of dissolved silicon (DSi) in the Xiangxi River and Poyang Lake basins were significantly lower than those in the Jiazhu River and the Ganjiang River, while the dissolved total carbon (DTC) and dissolved organic carbon (DOC) concentrations showed opposite results. The trend of C/Si ratio with seasonal change showed the decreasing and then increasing, wherein the west Poyang Lake were higher than the east. The DTC and DOC concentrations in winter were higher than those in other seasons. The effects of C and Si on the distribution characteristics of phytoplankton depended on watershed scale. The phytoplankton in the Jiazhu River was mainly affected by C, and the diatoms were most sensitive to the change of dissolved inorganic carbon (DIC) concentration. While in the Ganjiang River basin, Si was the main factor affecting the distribution of phytoplankton. After flowing into the Poyang Lake, the influence of Si on the distribution of phytoplankton became small. Overall, the DIC was not the limiting factor for phytoplankton growth in Poyang Lake watershed, but it could indirectly affect phytoplankton community structure by influencing the pH of water. The density of phytoplankton increased exponentially with the increase of the watershed scale. The density of phytoplankton in the Poyang Lake was about 11 times than that of the Jiazhu River, so the ecological environment and water pollution problems for the lake cannot be ignored.