This study establishes an eco-friendly anti-wrinkle treating process for cotton fabric. Sodium hydroxide-liquid ammonia pretreatment followed by 6% (w/w) PU100 adding citric acid pad-cure-dry finishing. In this process, citric acid (CA) was used as the fundamental crosslinking agent during finishing because it is a non-formaldehyde based, cost-effective and well wrinkle resistance agent. Environmental-friendly waterborne polyurethane (WPU) was used as an additive to add to the CA finishing solution. Six commercial WPUs were systematically investigated. Fabric properties like wrinkle resistance, tensile strength retention, whiteness, durable press, softness, and wettability were well investigated. Fourier transform infrared spectra and X-ray diffraction spectra were also measured and discussed before and after adding waterborne polyurethane. Tentative mechanism of the interaction among the WPU, CA, and modified cotton fabrics is provided. The effect of cotton fabric pretreatment on fabric performance was also investigated. After the eco-process’s treatment, the fabric wrinkle resistant angle was upgraded to 271 ± 7°, tensile strength retention was maintained at 66.77% ± 3.50% and CIE whiteness was elevated to 52.13 ± 3.21, which are much better than the traditional CA anti-wrinkle finishing based on mercerized cotton fabrics. This study provides useful information for textile researchers and engineers.