With the increasing demand for marine resources, the marine ecological environment system is gradually destroyed. The traditional allocation of marine resources has been unable to meet the global resource search, resulting in poor distribution uniformity of marine resources and high packet loss rate of resource allocation. Therefore, an optimal allocation method of sea resources based on ecological environment protection is proposed. Based on the concept of ecological protection, this method builds an evaluation index system for the allocation of Marine resources by measuring the loss of Marine spatial resource assets, and calculates the evolution trend and coordination of Marine ecology according to the weight of evaluation index. A robust optimization method for the optimal allocation of sea resources is established by obtaining the spatial differences in the allocation of sea resources. The experimental results show that the proposed method is more uniform in the distribution of sea resources and has a lower packet loss rate.