In the context of the increasing frequency and intensity of natural disasters, assessing the risk of typhoon disasters can provide significant assistance for risk control and emergency management of typhoon disasters. In this paper, based on the three-dimensional information diffusion method, the formal expected loss model is transformed into a computable typhoon risk assessment model. The fuzzy information in the small sample data is deeply mined, and the typhoon disaster risk assessment with the expected loss as the connotation is carried out, and the probability density distribution estimation of disaster-causing factors at different levels and the functional relationship identification between disaster-causing factors at different levels and direct economic loss rate are realized by using the information matrix. At the same time, combined with the frequency of typhoon occurrence, the annual risk of disasters is predicted to make up for the problem of insufficient marine environmental data and improve the calculation accuracy of risk assessment models. Taking Guangdong Province as an example, a typhoon risk assessment was conducted, estimating the probability distribution, direct economic loss rate distribution, and annual loss expectation of typhoon disasters under different wind speed scales and extreme wave heights. The results indicate that the risk estimation value of the three-dimensional information diffusion model is higher than that of the traditional model, which weakens the limitations of the low-dimensional information diffusion model and makes the evaluation results more reasonable and reliable.