The flight of bats is comparatively less documented and understood than birds and insects and may provide novel inspiration for the design of flapping flight robots. This study captured the natural flight of short-nosed fruit bats (Cynopterus sphinx) by an optical motion capture system, “OptiTrack”, with pasted markers on the wings and body to reconstruct the flight parameters. Due to the self-occlusion at some moments, points on the membrane wings cannot be captured by any cameras. To draw a smooth trajectory, it is desired to reconstruct all missing data. Therefore, an algorithm is proposed by using numerical techniques, accompanied by modern mathematical and computational tools, to envisage the missing data from the captured flight. The least-square fitted polynomial engendered the parameter equations for x-, y-, and z-coordinates of marked points which were used to reconstruct the trajectory of the flight. The parameter equations of position coordinates were also used to compute the morphological and aerodynamic characteristics of the flight. The most outstanding contribution of the work is that not only the trajectory, velocity, and velocity field but also the morphing areas of the membrane wings were recreated using the reconstructed data. These data and reconstructed curves of trajectory and velocity field will be used for the further aerodynamic analysis and mechanism design of the flapping robot. This method can also be generalized to reconstruct the performance parameters of any other animals for bionic design.