This paper establishes shipping enterprises’ safety culture system model based on the dynamic calculation matrix model. This paper calculates the deep learning theory’s shipping safety early warning system. At the same time, we use the fuzzy evaluation method to establish the relevant weights of the safety culture index system. The method model mentioned in this paper effectively avoids the subjectivity of the pure expert evaluation method. We use experimental simulations to verify the effectiveness of our model. Experiments show that the system in this paper has the advantages of reliable prediction results and high precision.