In this research, we numerically investigated the influences of the body’s presence on flow around the hovering fruit fly with regularized lattice Boltzmann method. In recent years, insect’s flapping flight system has been investigated because their superior flight mechanisms are expected to improve the flight abilities of micro air vehicles. Because of the simplification of experimental equipment and computational simulation, the insect model without body is often used to investigate the flow around the hovering flight insect. However, the gap between the wing and body can significantly change the flow around the wing root. Thus, we conducted investigations of the influences of the body’s presence on the vortical flow structure and cycle-averaged lift coefficient. As a result, the aerodynamic forces on the wings were enhanced by the body’s presence. The flow at the gap between wing and body enhanced the vortex strength and aerodynamic forces on the wing root region. Also, the cycle-averaged lift coefficient of the with body model was slightly higher than that of the without body model. If the wing’s flapping motion or the shape of the wing is changed, the effects of the body’s presence will cause different flow around the wing root. Therefore, it is necessary to take body’s presence into consideration.