Lake Qilu, a typical eutrophic plateau lake, the microcystin (MC) pollution caused by algal blooms in it will harm lake ecosystem and increase human health risks. To assess the pollution status and health risks of MCs in Lake Qilu Basin in autumn and winter, the surface water of Lake Qilu and seven major rivers entering the lake were sampled and analyzed, the temporal and spatial distribution characteristics of MCs isomers were analyzed. The relationship between MCs and water quality, phytoplankton and other environmental factors was investigated. The health risk posed by MCs was evaluated by human non-carcinogenic health risk. Our investigation results showed that MCs concentration decreased from autumn to winter. In autumn, IMCs accounted for more than 99%, and in winter, IMCs concentration was close to EMCs concentration. MC-RR and MC-LR were the main MCs isomers. The concentration ratio of MC-RR in autumn was higher than those of MC-LR and MC-YR. MC-LR concentration in winter was the highest. MCs was positively correlated with Microcystis density and other biological factors, and negatively correlated with TN, TP and NH₃-N nutrients. The risk index of MCs pollution in Lake Qilu ranged from 0.004 to 0.110, i.e., very low or low risk level. The risk in winter was slightly higher than that in autumn. Further attention should be paid to the risk caused by EMCs pollution on the south bank and IMCs release in the lake.