Schistosomiasis is a water-borne parasitic disease distributed worldwide, while schistosomiasis japonica localizes in the People’s Republic of China, the Philippines, and a few regions of Indonesia. Although significant achievements have been obtained in these endemic countries, great challenges still exist to reach the elimination of schistosomiasis japonica, as the occurrence of flooding can lead to several adverse consequences on the prevalence of schistosomiasis. This review summarizes the influence of flooding on the transmission of schistosomiasis japonica and interventions responding to the adverse impacts from the One Health perspective in human beings, animals, and the environment. For human and animals, behavioral changes and the damage of water conservancy and sanitary facilities will increase the intensity of water contact. For the environment, the density of Oncomelania snails significantly increases from the third year after flooding, and the snail habitats can be enlarged due to active and passive diffusion. With more water contact of human and other reservoir hosts, and larger snail habitats with higher density of living snails, the transmission risk of schistosomiasis increases under the influence of flooding. With the agenda set for global schistosomiasis elimination, interventions from the One Health perspective are put forward to respond to the impacts of increased flooding. For human beings, conducting health education to increase the consciousness of self-protection, preventive chemotherapy for high-risk populations, supply of safe water, early case finding, timely reporting, and treating cases will protect people from infection and prevent the outbreak of schistosomiasis. For animals, culling susceptible domestic animals, herding livestock in snail-free areas, treating livestock with infection or at high risk of infection, harmless treatment of animal feces to avoid water contamination, and monitoring the infection status of wild animals in flooding areas are important to cut off the transmission chain from the resources. For the environment, early warning of flooding, setting up warning signs and killing cercaria in risk areas during and post flooding, reconstructing damaged water conservancy facilities, developing hygiene and sanitary facilities, conducting snail surveys, using molluscicide, and predicting areas with high risk of schistosomiasis transmission after flooding all contribute to reducing the transmission risk of schistosomiasis. These strategies need the cooperation of the ministry of health, meteorological administration, water resources, agriculture, and forestry to achieve the goal of minimizing the impact of flooding on the transmission of schistosomiasis. In conclusion, flooding is one of the important factors affecting the transmission of schistosomiasis japonica. Multi-sectoral cooperation is needed to effectively prevent and control the adverse impacts of flooding on human beings, animals, and the environment.