The inertia plays a significant role in the response of a system undergoing flow-induced vibrations, which has been extensively investigated by previous researchers. However, the inertial effects of an energy harvester employing the mechanism of flow-induced vibrations have attracted little attention. This paper concentrates on a semi-passive energy extraction system considering its inertial effects. The incompressible Navier-Stokes equations are solved using a finite-volume based numerical solver with a moving grid technique. A partitioned method is used to couple the fluid and structure motions with the sub-iteration technique and an Aitken relaxation, which guarantees a strong fluid-structure coupling. In addition, a fictitious mass is added to resolve the numerical instability aroused by low density ratios. First, at a fixed mass ratio of r = 1, we identify an optimal set of parameters, at which a maximum efficiency of η = 34% is achieved. Further studies with r ranging from 0.125 to 100 are performed around the optimal parameters. The results show that for the semi-passive flapping energy harvester, the energy harvesting efficiency decreases monotonically with increasing mass ratio. We also notice that the total power extraction stays at a high level with little variation for r < 10; therefore, if we concern more about the amount of power extraction rather than its efficiency, the inertial effects can be neglectable for r < 10. Moreover, since one degree of freedom is released for the semi-passive system, it is possible for the system to automatically determine its optimal operational parameters. We note that the optimal phase difference ϕ = 82° has been well determined, which leads to a good timing of vortex-foil interactions. We note two different trends on phase difference for the effects of reduced frequency and mass ratio, respectively. By varying the reduced frequency f∗, an optimal f∗ is identified, at which the minimum phase difference is achieved. While the relationship between phase difference and mass ratio is monotonic, a maximum phase difference is achieved at the nearly zero mass ratio. Nevertheless, both trends point to the same optimal phase difference, i.e., ϕ = 82° at θ0 = 75°. Furthermore, the relationship between the leading edge vortex and the phase difference is systematically investigated, accounting for the physical reason of existence of the optimal phase difference.