Penguins use the wings (flippers) to swim underwater and demonstrate excellent capability such as long-distance travel and agile maneuvers for foraging or escaping. Although previous 2-D kinematics studies depicted the basic lift-based propulsion mechanism, the details of the 3-D wing kinematics, wing deformation, and thrust generation mechanism are largely unknown. In this study, we reconstructed the 3-D kinematics of a gentoo penguin (Pygoscelis papua) in slow forward swimming at an aquarium using multidirectional videos recorded by twelve underwater cameras. We also conducted water tunnel experiments with a 3-D printed wing to obtain its lift and drag coefficients for various angles of attack. Combining the obtained kinematics and hydrodynamic force characteristics, the thrust of the wings was calculated in a quasi-steady manner. In the calculation, the effect of the wing deformation was evaluated by comparing the following two cases: (1) an original case where the wing kinematics include original bending deformation; and (2) a rigid case where the wing was flattened. The kinematic measurements revealed that the wings are dynamically bent in accordance with flapping, which decreases the magnitude of angle of attack during both upstroke and downstroke. Moreover, the comparison of the original and rigid cases demonstrated that greater thrust was generated in the original case, where the excess angle of attack is suppressed by the wing bending. The present study provides a qualitative mechanism of lift-based propulsion in penguins and imply the importance of wing bending on thrust generation.