The risk of marine disasters based on flooding is one of the most significant natural disasters in coastal zones. It can be said that flooding in coastal zones has typical sea–land characteristics. Yet, relatively little research has been done in this area. Thus, by using the characteristics of marine disaster risk based on flooding in Qingdao and combining marine science and land science methods, this paper constructs a targeted indicator system for the flooding risk from marine disasters from the perspectives of the disaster natural chain and flooding process. According to the results, the Integrated Risk Index of marine disasters based on flooding in Qingdao is 0.3694, which represents a medium risk level for natural disasters in China’s major coastal areas. The first- and third-level indicators with large contribution rates are almost all natural indicators. This indicates that the natural disaster process and disaster chain greatly affect the flooding disaster risk in Qingdao. However, although natural factors play large roles in the risk of disaster, preventive methods implemented by humans can still have a positive effect on disaster reduction. Therefore, human society should still proceed with understanding disasters from natural processes, change their passive response to active adaptation, and actively strengthen preventive measures to alleviate the adverse impacts of increasingly serious natural disasters.