Electromagnetic compatibility evaluation is an important technical measure in the warship design and efficiency evaluation, and guarantees the electron equipment and electric equipment be work together without any performance decline. This paper analyzes the present evaluation methods’ disadvantages, and brings forward an improved multi-hierarchical weighing additive summation method. This method adopts standard deviation weighing measures distributing weight, which belongs to external investiture weigh and avoid subjective because of lack of uniform external criterion. Improved multi-level hierarchies weighing additive summation method normalizes the quantification technical target and make qualitative technical target impersonal. This method solves the evaluating problem in complex target system of multi-object, multi-level hierarchies, asymmetry, and multi-conditional. To validate the improved method, one design proposals for a particular warship model are evaluated. The results indicate that the presented approach is suitable for analyzing complicated systems such as warship.