The middle route of South-to-North Water Diversion Project has been the main source of water supply for Beijing and Tianjin since its opening to the outside world, bringing massive social and economic benefits to the society. At present, the physical and chemical indices of water quality are relatively stable in the middle route project, with occasional abnormal algal proliferation in some channel sections, which may lead to algal blooms if left unattended. To address this problem, the engineering measure of local cooling ventilation, which changed the local meteorological conditions was adopted, and a two-dimensional hydrodynamic and water quality model was developed for the Penghe-Shahe aqueduct, and the effects of different ventilation locations, ventilation temperature and ventilation duration on water temperature and algae growth in water diversion channels were studied. The results show that both water temperature and chlorophyll a concentration are related to ventilation position, ventilation temperature and ventilation duration. The lower the ventilation temperature, the longer the ventilation duration, the greater the decline of the water temperature and chlorophyll a concentration, the water temperature can be reduced by about 2 ℃, and the concentration of chlorophyll a can be reduced by about 54.5% at most, both upstream only ventilation and whole channel section ventilation can lower the water temperature and inhibit the growth of algae, but downstream only ventilation has little effect on water temperature and algae growth. Therefore, local cooling can reduce the concentration of chlorophyll a to some extent, considering the algal inhibition effect and engineering cost, the engineering measure of local cooling ventilation in the upstream is recommended for the algal bloom-prone channel sections.