Penguins are adapted to underwater life and have excellent swimming abilities. Although previous motion analyses revealed their basic swimming characteristics, the details of the 3D wing kinematics, wing deformation and thrust generation mechanism of penguins are still largely unknown. In this study, we recorded the forward and horizontal swimming of gentoo penguins (Pygoscelis papua) at an aquarium with multiple underwater action cameras and then performed a 3D motion analysis. We also conducted a series of water tunnel experiments with a 3D printed rigid wing to obtain lift and drag coefficients in the gliding configuration. Using these coefficients, the thrust force during flapping was calculated in a quasi-steady manner, where the following two wing models were considered: (1) an ‘original’ wing model reconstructed from 3D motion analysis including bending deformation and (2) a ‘flat’ wing model obtained by flattening the original wing model. The resultant body trajectory showed that the penguin accelerated forward during both upstroke and downstroke. The motion analysis of the two wing models revealed that considerable bending occurred in the original wing, which reduced its angle of attack during the upstroke in particular. Consequently, the calculated stroke-averaged thrust was larger for the original wing than for the flat wing during the upstroke. In addition, the propulsive efficiency for the original wing was estimated to be 1.8 times higher than that for the flat wing. Our results unveil a detailed mechanism of lift-based propulsion in penguins and underscore the importance of wing bending.