To investigate the effects of proanthocyanidins (PA), myricetin, resveratrol, and kaempferol on the modification of dentin collagen and the inhibition of matrix metalloproteinase (MMP) activity, and to evaluate their contributions to the biomimetic remineralization and resin-dentin bonding performance. Attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) and in situ zymography were applied to verify the collagen modification and MMP activity inhibition induced by these four polyphenols. Scanning electron microscopy/energy dispersive spectrometer (SEM/EDS) analysis, X-ray diffraction (XRD), ATR-FTIR, Vickers hardness numbers (VHN), and micro-computed tomography (micro-CT) were performed to characterize the remineralized dentin. Microtensile bond strength (μTBS) and nanoleakage were investigated to evaluate the effects of the four polyphenols on resin-dentin bonding durability. ATR-FTIR and in situ zymography confirmed that these four polyphenols could modify dentin collagen and inhibit MMP activity, respectively. Chemoanalytic characterization exhibited the efficacies of the four polyphenols in promoting dentin biomimetic remineralization. The surface hardness of PA-pretreated dentin was the greatest. Micro-CT results demonstrated that the PAs group possessed the highest amount of dentin surface minerals and the lowest amount of deep-layer minerals. The surface and deep-layer mineral contents of the Myr group were higher than Res and Kae groups. Treatment with these four polyphenols significantly increased the initial μTBS compared with the control group without primer conditioning. μTBS decreased significantly during aging, and the decrease was more severe in the PAs and Kae groups than in the Myr and Res groups. With or without aging, the polyphenol groups exhibited relatively less fluorescence. However, the Myr and Res groups showed less serious nanoleakage after aging. PA, myricetin, resveratrol, and kaempferol can modify dentin collagen, inhibit MMP activity, promote biomimetic remineralization, and improve resin-dentin bond durability. Compared with PA and kaempferol, myricetin and resveratrol are more effective in improving resin-dentin bonding.