Background: Reliable bonding between resin composite restorations and deciduous dentin is clinically challenging. Theaflavins (TFs), black tea-derived natural polyphenols with collagen cross-linking, matrix metalloproteinase (MMP)-inhibiting and antibacterial activities, have not been studied as a deciduous dentin pretreatment agent. This study evaluated 2% (w/v) TFs for improving bond strength and marginal sealing, with 2% chlorhexi dine (CHX) and distilled water (DW) as controls. Methods: Forty-eight caries-free primary molars were randomly assigned to micro-tensile bond strength (µTBS, 30 teeth) or microleakage (18 teeth) testing. Each group was subdivided into TFs, CHX, and DW subgroups, and these were further split into immediate/aged testing. After pretreatment and adhesive/resin application, µTBS measurement, fracture mode observation, interface morphology analysis, and International Organization for Standardization (ISO)-standard microleakage assessment were conducted; data were analyzed via SPSS 26.0 (α = 0.05). Results: µTBS: In both immediate and aged groups, TFs group depicted the highest strength, followed by CHX and DW (p < 0.05). Fracture mode: After aging, the DW group showed predominantly type I interfacial failure, while the CHX and TFs groups displayed fracture mode III—a mode not observed in the DW group. Interface morphology: TFs group had the most and longest resin tags, while the thickest and most intact hybrid layer were observed in both immediate and aged groups. Microleakage: In both immediate and aged groups, the TFs group was lower than DW (p < 0.05) but showed no significant difference from CHX group (p > 0.05). TFs group had no significant change in microleakage after aging (p > 0.05). Conclusions: The 2% TFs pretreatment significantly improved bond strength and reduced microleakage in deciduous dentin, as compared with those with 2% CHX.