Abstract: It is urgent to analyze the effect of solar shortwave radiation reduction caused by water photovoltaic on alleviating algae proliferation in open channels. Taking the middle route of South-to-North Water Diversion project as an example, the hydrodynamic and water quality coupling model of the main canal from Anyang River control gate to Fenzhuang River control gate was established. The influence of solar shortwave radiation reduction caused by water photovoltaic covering on the open channel and the influence of different cover positions on water temperature and water quality were analyzed and compared. The coupling effect of flow velocity and solar shortwave radiation on algae biomass was studied. The results showed that when carrying out the water photovoltaic project, the reduction of the solar shortwave radiation received by the channel will lower the water temperature, algae biomass and dissolved oxygen concentration, but increase the nutrient concentration. When the solar shortwave radiation decreases by 50%, the algae biomass begins to reduce gradually. Under the same coverage rate and transmittance scenario, the peak reduction differences of algae biomass among different covering locations are small. When the solar shortwave radiation amount gradually changes from high to low, the influence degree of velocity change on algae biomass shows a trend of first increasing and then decreasing.