To address the poor adhesion of waterborne inks to polyethylene terephthalate (PET) films, a low-temperature ketone–hydrazide self-crosslinking system based on 2-(acetoacetoxy)ethyl methacrylate (AAEM) and adipic acid dihydrazide (ADH) was incorporated into a waterborne polyurethane–acrylate emulsion. Self-crosslinking waterborne polyurethane–acrylate emulsions (AWPUAs) with different AAEM contents were prepared and subsequently used as binders in waterborne inks for PET films. The results showed that increasing the AAEM content reduced the water absorption of the latex films while increasing their water contact angle and tensile strength. Meanwhile, the adhesion of the resulting waterborne inks to corona-treated PET films increased with increasing AAEM content, together with a substantial enhancement in re-solubility. At an AAEM content of 7 wt%, the AWPUA emulsion exhibited good colloidal stability, and the corresponding waterborne ink achieved nearly 100% adhesion while maintaining good re-solubility. These findings demonstrate that AAEM/ADH ketone–hydrazide self-crosslinking modification provides an effective approach for improving the film properties of waterborne polyurethane–acrylate emulsions and the application performance of waterborne inks on PET films.