Producing high-efficient, low-cost, and green water-based adhesives with enhanced bonding performance still remains highly challenging. In this study, waterborne polyurethane (WPU) adhesive films with long-term stability are in situ fabricated on a metal substrate by a facile and high-efficiency preparation method known as demulsification-induced fast solidification (DIFS). The bonding strength of adhesive films was enhanced by constructing multiple cross-linked structures between polycarbodiimide (PCD) and WPU, which determines the cohesive force of the adhesive films. The bonding strength obtained for WPU-L/PCD-0.1 (L: polycaprolactone, 0.1 represents the PCD mass fraction to emulsion) adhesive film is>2.40 ± 0.21 MPa (stock-break failure mode) at room temperature for 120 d, satisfactory for stable connections. Moreover, the cross-linked adhesive film exhibits an excellent water-resistance performance because PCD and hydrophilic carboxyl groups of WPU form a cross-linking network to eliminate the hydrophilic carboxyl groups. We expect that this new type of adhesive film will be useful for metal bonding and metal protection coatings applications.