Structural degeneration of a hybrid layer composed of a demineralized dentin matrix (DDM) and adhesive causes unsatisfactory functional outcomes in terms of bonding repair and caries treatment and is accompanied by high prevalence of secondary caries. Clinically, defects in the hybrid layer from insufficient adhesive infiltration, bacterial load from retained infected-dentin, and bacterial attack from the oral cavity are the main threats to degeneration. Currently, there is no strategy to simultaneously address adhesive penetration and bacterial infection. Herein, based on the core role of the strongly-polar hydrated DDM interface in dentin bonding, an interface-reconstructed bonding strategy assisted by electrostatic assembly of broad-spectrum germicidal polyhexamethylene biguanide (PHMB) is proposed that kills two birds with one stone. PHMB is absorbed onto the anionic 3D DDM forming a PHMB/DDM complex. The surface potential of the DDM increases by about 100 mV, the anion content decreases by 20%, and the interface water content decreases by nearly 40%. All of these changes contribute to the penetration of the adhesive, thereby improving the bonding strength and durability. After thermal cycling aging, the bonding strength of the PHMB group was 1.45–1.65 times that of the control group. In terms of antibacterial properties, PHMB treatment not only has a bacterial-killing ability due to the already formed biofilm but also significantly reduces the adhesion of bacteria, thereby delaying the occurrence of secondary caries. In summary, PHMB treatment reconstructed the DDM interface, resulting in a defect-low and inherent antibacterial hybrid layer that improves the bonding effect, treatment of caries and even prevention of secondary caries.