To protect tomato pulp quality, this study investigated the effect of the infrared peeling method (using our newly developed catalytic infrared peeling equipment) on pectin's chemical, structural and functional properties and their correlation compared with manual, hot-water, and lye peeling methods. Infrared peeling significantly improved pectin’s emulsifying and antioxidant capacity compared to manual peeling by increasing branching degree. Hot water peeling significantly improved pectin’s viscosity, emulsifying and antioxidant capacity. However, the pectin chains had low flexibility. The effect of lye peeling on pectin was the greatest, causing the lowest linearity and the largest degree of branching. In comparison, infrared peeling had the least impact on pectin. It was further confirmed that pectin’ viscosity, emulsifying, and antioxidant capacity were highly correlated with its chemical and structural properties. In summary, the infrared peeling method provides better pulp quality and is more sustainable because no water and chemicals are used.