Shallow water cage culture is the main marine activity of Xincun Lagoon, Hainan. However, the continuous growth of aquaculture activities not only aggravates the deterioration of the ecological environment of Lagoon, but also affects the healthy development of mariculture. Suitability analysis on net cage mariculture can reduce the pressure of marine ecological environment, increase the yield of aquaculture and alleviate the conflict between different marine activities to a certain extent. However, the interaction of various factors affecting the suitability evaluation of mariculture constitutes a complex system, and the traditional method of weight determination cannot fit the actual situation well. For this reason, this paper attempts to introduce the interaction matrix of rock engineering systems (RES) to evaluate the weight of each index. At the same time, a multi-criteria decision analysis (MCDA) model based on GIS is established. Finally, a continuous graph of the suitability change of shallow sea cage culture in Xincun Lagoon is obtained. The results show that (1) the entrance area of Lagoon is the most suitable area for cage culture in shallow water; (2) the evaluation results are in agreement with the actual situation and previous studies, and the weight determination method is reasonable and feasible.