In this work, direct numerical simulation (DNS) is used to investigate how airfoil shape affects wake structure and performance during a pitching-heaving motion. First, a class-shape transformation (CST) method is used to generate airfoil shapes. CST coefficients are then varied in a parametric study to create geometries that are simulated in a pitching and heaving motion via an immersed boundary method-based numerical solver. The results show that most coefficients have little effect on the propulsive efficiency, but the second coefficient does have a very large effect. Looking at the CST basis functions shows that the effect of this coefficient is concentrated near the 25% mark of the foils chord length. By observing the thrust force and hydrodynamic power through a period of motion it is shown that the effect of the foil shape change is realized near the middle of each flapping motion. Through further inspection of the wake structures, we conclude that this is due to the leading-edge vortex attaching better to the foil shapes with a larger thickness around 25% of the chord length. This is verified by the pressure contours, which show a lower pressure along the leading edge of the better performing foils. The more favorable pressure gradient generated allows for higher efficiency motion.