A major safety factor in marine reactor design, critical heat flux (CHF), is assessed using the MARS system analysis code under heaving conditions. As gravity acceleration changes, the CHF is affected by the thermal hydraulics in the reactor through inlet flow fluctuations. Performing the analysis with the MARS code, which uses the properties of water for the working fluid, requires applying the CHF experimental data using fluid-to-fluid (FTF) scaling because most CHF experiments are conducted with Freon (R-113) as the working fluid. The FTF scaling methods suggested by Ahmad, Katto, and Coffield are adopted and compared. Otsuji et al.'s experiment, which was conducted using mass flow rate oscillation, is applied to evaluate the capability of MARS for heaving conditions. According to the calculations the FTF methods of Ahmad, Katto, and Coffield show good agreement (within an error of ±10.73% for Otsuji et al.'s experiment) for inlet flow rate oscillation corresponding to gravity acceleration in a vertical direction. In addition, variation of the acceleration affects the flow conditions, such as the mass flow rate and the void fraction. Thus, MARS has a noteworthy ability to predict the CHF for heaving conditions by simulating inlet flow rate oscillation.