Objective: To investigate the ability of different concentrations of piceatannol (PIC) solution to biomodify decalcified dentin matrices in primary teeth, thereby providing a theoretical basis for improving the durability of resin-dentin bonding. Methods: This study was approved by the Medical Ethics Committee of the institution. Molecular docking was performed to predict the interaction effects of PIC with type I collagen and matrix metalloproteinases (MMPs) in dentin. A total of 124 clinically extracted intact primary molars were selected due to retention; of these, 76 were prepared into 60 completely decalcified dentin beams and 24 dentin slices. The 60 beams were equally allocated for dry mass loss and swelling ratio testing (30 beams each). For both experiments, the beams were randomly divided into five groups (n = 6): a control group, 5% glutaraldehyde group, and 2.5, 5, and 10 mg/mL PIC solution groups. This was to evaluate the anti-enzymatic hydrolytic properties and mechanical performance of type I collagen. Of the 24 slices, 15 were assigned to the aforementioned five groups (n = 3) for Fourier-transform infrared spectroscopy (FTIR) to explore the cross-linking mechanism. The remaining nine slices were randomly divided into three groups (n = 3): distilled water group A (SEM examination prior to enzymatic hydrolysis), distilled water group B (SEM examination after enzymatic hydrolysis), and a 10 mg/mL PIC solution group (SEM examination after treatment with 10 mg/mL PIC and subsequent enzymatic hydrolysis). This was to evaluate the cross-linking effect on demineralized dentin collagen. The remaining 48 molars were fabricated into bonding specimens and randomly divided into four groups (n = 12): a control group (distilled water group) and 2.5, 5, and 10 mg/mL PIC groups. Immediate and aged shear bond strength (SBS) were measured, and failure modes were observed under a stereomicroscope to investigate the impact of different PIC concentrations on the bonding durability of primary tooth dentin. Results: Molecular docking revealed strong binding activity between PIC and type I collagen/MMPs via hydrogen bonds, electrostatic potential, and hydrophobic forces; the FTIR results confirmed hydrogen bond formation. In the dry mass loss test, mass loss rates in the 2.5, 5, and 10 mg/mL PIC groups were significantly lower than that in the control group (P < 0.05), with the 10 mg/mL PIC group showing the most optimized cross-linking effect. Swelling tests indicated that all three PIC concentrations reduced the swelling ratio of the demineralized matrix, effectively improving its mechanical properties. SEM showed that collagen from the 10 mg/mL PIC group retained its natural three-dimensional network post-enzymolysis, contrasting sharply with the disintegrated collagen in the enzymolyzed distilled water group B but resembling the morphology of the non-enzymolyzed distilled water group A. SBS results demonstrated that the 10 mg/mL PIC group exhibited significantly higher bond strengths than the control group in both the immediate and aged tests (P < 0.05); immediate SBS in the 10 mg/mL PIC group was also significantly greater than that in the 2.5 mg/mL PIC group (P < 0.05), while no other intergroup differences were found (P > 0.05). Failure mode analysis indicated predominantly mixed fractures, with the proportion of interfacial fractures decreasing as PIC concentration increased compared with the control group. Conclusion A 10 mg/mL PIC solution can effectively cross-link decalcified dentin matrices in primary teeth, enhancing the anti-enzymatic hydrolytic capacity and mechanical properties during clinical operation, thereby promoting bond strength and interface stability, which promises to improve the long-term durability of resin-dentin bonding.