Fish swimming has attracted attention as a locomotion system with excellent propulsive efficiency. They swim by moving their body, fins, and other organs simultaneously, which developed during evolution. Among their many organs, the pectoral fin plays a crucial role in swimming, such as forward–backward movement and change of direction. In order to investigate the hydrodynamic interaction between pectoral fins and fish bodies, we examined the asymmetric flapping motion of the pectoral fin concerning the body axis and investigated the effect of the pectoral fin on the propulsive performance of the body of a small swimming object by numerical simulation. In this study, the amplitude ratio, frequency ratio, and phase of the body and pectoral fin varied. Therefore, although propulsive performance increased in tandem with the frequency ratio, the amplitude ratio change had negatively affected the propulsive performance. The results revealed that the propulsive performance of the fish was high even in low-frequency ratios when the phase difference was varied. The highest propulsion efficiency increased by a factor of about 3.7 compared to the phase difference condition of 0.