The double-bottom cages for flounder fish tend to move and deform under waves. Therefore, it is necessary to carry out hydrodynamic analysis for the stabilization of flounder fish cages. Herein, a numerical model of deformation of double-bottom cages under waves was established based on the finite element method, and then maximum displacement and the pitch of the double-bottom were calculated. First, results of the upper bottom were compared with that of the lower bottom. Afterwards, the results of the lower bottom of double-bottom cage were compared with that of the single-bottom cage. The simulation results showed that the two bottoms of double-bottom cages were able to stay relatively parallel during wave periods. The maximum displacement and pitch of the two bottoms increased along with not only wave height but also wave period. In addition, the inclined direction of the two bottoms was the same. Under the same wave conditions, the horizontal of displacement and the maximum pitch of lower bottom were larger than those of the upper bottom, but their vertical displacements were not much different. It was found that the difference in pitch between upper and lower bottoms was the largest when the wave height was 15 cm and the wave period was 1.4 s. However, the upper and lower bottoms of the cage did not collide with each other, and the two bottoms of the cage could remain relatively stable. Moreover, under the same wave conditions, the displacement of the lower bottom of the double-bottom cage was less than that of the single-bottom cage, but the pitch of the lower bottom of the double-bottom cage was larger than that of the single-bottom cage. Additionally, the maximum mooring-line force of double-bottom cages for flounder fish was larger than that of single-bottom cages. Furthermore, the study on the hydrodynamic characteristics of double-bottom cages for flounder fish under the combined action of wave and flow should be carried out in the future.