In order to achieve the goal of energy conservation and environmental protection, the main engine exhaust residual heat refrigeration unit was installed on the fishing vessel for reuse of the exhaust from the main engine. During the operation, cracks occurred in the generator enclosure bulkhead of the refrigeration equipment. It is necessary to analyze the cause of the cracks and give the solution. CFD fluid analysis software was used to analyze the smoke velocity and pressure of the generator. The results showed that the smoke velocity and pressure had little effect on the enclosure bulkhead. Then the inherent modal of the generator structure was analyzed, and the structure form was changed by increasing the thickness of the enclosure bulkhead, so as to change the natural frequency of the structure until there is no overlap between the structural frequency band and the original structural frequency band. Since the thickness avoids the frequency range that causes resonance, a new stainless steel plate with enclosure bulkhead thickness of 3mm is selected to replace the original one of 1.5mm for making a new enclosure bulkhead for the equipment. In the design of equipment structure, especially the structure of small load fluid motion, the natural frequency of the structure should be analyzed to avoid its overlap with excitation frequency of the fluid motion, causing resonance and damage to the structure.