In this paper, among the various facilities used in marine farming, young bivalves of the Mytilus galloprovincialis of marine farming was placed on the deck of the fishing vessel to evaluate the environment conditions and drive shaft movement by rolling affecting the separator for the young bivalves and a clean process. There were a few studies on stress analysis of development facilities because it was difficult to access the fishing site due to the use of imported equipment and the lack of development of domestic equipment. In this study, stress analysis of the fixed part of separator for young bivalves and its adjacent part was performed on various phases when the vessel was tilted by rolling using the finite element method. In addition, the structural safety of the internal blade under the driving conditions according to the movement of the drive shaft by the hydraulic motor was confirmed through structural analysis. As a result, the connection part between the deck and the separator by rolling was confirmed to have higher stress than that of other parts due to stress concentration. In addition, it was confirmed that the maximum stress occurred on the connection part between blades. Even though the safety of the separator for marine farming was confirmed by structural analysis, it is necessary to comprehensively consider the age of vessels, the material of the deck, and the corrosion of the deck.