For offshore nuclear power platforms, complex ocean conditions may lead to flow instability and decrease the safety of the reactor. In this study, the trajectory analysis method is used to assess the stability of the system. The Fast Fourier Transform analysis method is applied to analyze the evolution process of flow fluctuations, and an analysis process is developed for the division of affected regions by flow instability under ocean conditions. The diagram of system operating condition can be quantitatively divided into different regions. The research results indicate that as the power increases, the system trajectory diagram composed of inlet and outlet flows undergoes an evolution process from a convergence loop to a self-sustained loop, and ultimately to a divergence loop. According to the flow fluctuation characteristics of flow instability evolution under ocean conditions, the diagram of system operating condition can be divided into ocean condition control region, joint control region, and flow instability control region. Additionally, the impact of maximum heaving acceleration on the region division is investigated. When the maximum heaving acceleration is relatively small, the ocean condition control region is smaller while the joint control region is larger. This study shows that the triggering mechanism of flow fluctuations under ocean conditions and provides guidance for the design and safe operation of systems in such environments.