The functional redundancy between multiple marine environmental monitoring systems leads to resource waste and unnecessary capital investment. Therefore, the systems should be integrated optimally into an organic whole to save resources and costs of marine environmental monitoring. In light of this, the Entropy method was introduced on the basis of linear programming and the marine environmental monitoring system was divided into different modules according to functions. Taking cost and efficiency index as the main object and through reasonable allocation, the construction cost can be reduced as far as possible while ensuring that the monitoring capability after optimization and integration is not reduced.