Pillow plate heat exchangers (PPHE) with compactness and high thermal performance are applying widely. In present article, PPHE with ellipse weld spots is first proposed, and turbulent flow and heat transfer of supercritical carbon dioxide (S-CO2) in PPHE channel is analyzed and optimized. The channel is made of many periodically overlapped metal plates, and the plate is a flat plate with many staggered convex-concave spots. Compared with channel section with concave spot, channel section with convex spot has higher flow velocity, lower flow fraction and higher heat transfer coefficient, so it dominates heat transfer process. Along flow direction, heat transfer coefficient in channel section with convex spot gradually increases to maximum in flat region, and then it drops to minimum in downstream region of convex spot, while friction factor has opposite tendency. A meaningful phenomenon is found that higher heat transfer coefficient (h) and lower friction factor (f) appear simultaneously in the same region. The flow and heat transfer behavior are significantly affected by weld spot geometries, and elliptic weld spot with larger ratio of spot length and width Ψ results in weaker vortices and fluid impingement, which remarkably reduces friction factor. The elliptic weld spot with Ψ = 1.4 is optimum geometry for maximum index of Nu/f1/3. In addition, correlations of f and Nusselt number (Nu) for Ψ = 0.6–1.4 and Re = 4132–6650 are developed.