In recent years, frequent high temperatures and heavy rainfall in summer in China have led to a large-scale reduction in Welsh onion (Allium fistulosum L.) production. This experiment used “Hanchuan” Welsh onion as test material to analyze the effect of high temperature and waterlogging on the dry matter quality, root structure, oxygen species (ROS) metabolism, and photosynthetic performance. The results showed that waterlogging or high-temperature stress could lead to a decrease in dry matter content and root activity in various parts of Welsh onion, significantly increasing the content of reactive oxygen species (ROS) in Welsh onion roots and leaves, accelerating membrane lipid peroxidation, and significantly reduce the chlorophyll content and photosynthetic performance of Welsh onion. Among them, the damage caused by waterlogging and high-temperature interaction stress to Welsh onion is the most significant. On the 8th day of treatment, the net photosynthetic rate (Pn) of high-temperature normal water supply, normal-temperature waterlogging, and high-temperature waterlogging decreased by 53.62%, 26.4%, and 87.59%, respectively, compared to the control. The results of this study provide insight into the extent of damage to Welsh onion under different moisture and temperature conditions, which will help explore scientific methods to alleviate the damage caused by high temperature and waterlogging in Welsh onion in the future.