A complicated coupling system performs fuel filling operation of a ship on the sea that involves tank sloshing and filling impact. This research elaborated on the sloshing load and flow characteristics of the variable mass tank and revealed its physical process through numerical simulations to provide safety assurance for fuel filling. First, this work clarified the difference between the numerical theory of variable mass tank sloshing and that of ordinary sloshing. On this foundation, a numerical model was developed for a three-dimensional variable mass tank sloshing. In addition, the model was validated by comparing the results of the previous experiments. Second, the sloshing pressure and internal free surface of the tank were monitored by numerical simulations. At the same time, a series of sensitivity analyses were carried out against the sloshing period, filling rate, and sloshing amplitude. Finally, the baffle was added to the sloshing tank to study the influence of internal barrier structure on the sloshing flow and pressure characteristics. The following conclusions were obtained from this work: Fuel filling caused an increase in liquid mass, suppressing sloshing and increasing the tank load. Overall, the sloshing load increased with the filling rate. Moreover, the impact of internal barrier structure on sloshing is discussed in this study, and it was discovered that the sloshing effect could be efficiently suppressed by the barrier structure.