Rubber can improve the mechanical properties of the coated nitrogen fertilizers (CNFs), but the biomass components cause holes in the urea release process, thus accelerating the release of urea. In this study, a self-healing rubber (SHR) shell/hydrogel core based on a supramolecular network was fabricated as a coating material for CNFs to improve the above problems. The core of CNFs consists of vanillin(Van)-cross-linked poly(vinyl alcohol) (PVA)/carboxymethyl chitosan (CMCS) hydrogel, prepared by a freeze−thaw cycle. The shell of CNFs was prepared by soaking Van-cross-linked natural rubber (NR)/chitosan (CS)/PVA material in Zn 2+ solution. A green core− shell structured CNF with hydrogen bonding and metal coordination was finally prepared, which has improved the mechanical properties, slow-release effect, and soil water retention capacity of the CNF. The effects of CS and PVA contents and the impregnation of Zn 2+ on the physical and chemical properties of the SHR supramolecular composite and its self-healing ability were investigated, and the urea release kinetics were analyzed. The CNFs could reach release equilibrium in water for 10 days, with a slow-release rate of 62.7%, and the urea release kinetics were in accordance with the Korsmeyer−Peppas model (R 2 ≥ 0.90), with a possible release mechanism of Fickian diffusion.