The utilization of floodwater resources will produce benefits, but it will also pose risks; therefore, it is necessary to strengthen knowledge regarding risk assessment to minimize negative effects. In the present study, the risk factors for the utilization of floodwater resources in water diversion projects were identified, the index system was constructed, and the fuzziness and randomness of the risk were considered. Assessment was performed with respect to the following three projects: water storage, water conveyance, and water pumping. The specific methods to improve the cloud model are as follows: analytic hierarchy process (AHP) is used to calculate subjective weights, entropy weight method and projection pursuit method are used to calculate objective weights, X-conditional cloud is used to calculate index membership degree, and finally combination weight and membership degree are combined to obtain the risk level of flood resource utilization. The above methodology was applied to the risk assessment of floodwater resources utilization in the Jiangsu Province of the East Route of the South-to-North Water Transfer Project. The risk of floodwater resources utilization in high-flow, normal-flow, and low-flow years was evaluated, and the validity and applicability of the assessment method were verified.