In very few studies it is shown that an increase in vertical force can be achieved when a flapping-wing hovers in ground effect (IGE). The body, however, has usually been neglected and its influence on three-dimensional vortex structures and consequent aerodynamic forces is still unclear. In this study we carried out a computational fluid dynamic study of a fruit fly (Drosophila melanogaster) hovering for two cases: “in ground effect” and “out of ground effect” (OGE), where the heights from the ground are less than one and more than five times the wing length, respectively. The wings in the IGE computation generated merely 0.7% larger wingbeat cycle-averaged vertical force than in the OGE condition. The body, in contrast, exhibited a significant increase in the vertical force: when out of ground effect, the average vertical force of the body was almost zero (-0.0025 μN); whereas in ground effect, the force increased to 0.78 μN, which is the major contributor to the 8.5% increase in the total vertical force (from 9.9 μN at OGE to 10.8 μN at IGE). Meanwhile, the aerodynamic power of the wings decreased by 1.6%, resulting in a 10% improvement in the overall vertical force-to-aerodynamic power ratio. The flow-field visualization revealed that the downwashes generated by the wings create a high pressure “air cushion” underneath the body, which should be responsible for the enhancement of the body vertical force production. Our results point to the importance of the presence of body in predicting the vertical forces in flapping flights in ground effect.