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Background: Lignin played an important role in the establishment of coated fertilizers coating material as a substitute for petrochemical raw materials. However, so far, the lignin-based coated fertilizers was limited in only the poor slow-release performance. To achieve good slow-release performance of lignin-based coated fertilizers, hydrophilic of lignin need to be resolved to establish an green and better controllable lignin-based coated fertilizers. Results: In the study, a novel green double layer coating with lignin-based polyurethane (LPU) as the inner coating and epoxy resin (EP) as the outer coating was effectively constructed for coated urea. Fourier transform infrared spectra confirmed that lignin and polycaprolactone diol successfully reacted with Hexamethylene diisocyanate. The loss weight and water contact angle (WCA, 75.6–63.6°) of the LPUs decreased with the increased lignin content. The average particle hardness of the lignin-based double-layer coated urea (LDCU) first increased from 58.1 N (lignin of 30%) to 67.0 N (lignin of 60%), but then decreased to 62.3 N (lignin of 70%). The release longevity of the coated urea was closely related to the preparation parameters of the coating material. The optimal cumulative nutrient release rate (79.4%) of LDCU was obtained (lignin of 50%, –CNO/–OH molar ratios of 1.15, EP of 35%, and coating ratio of 5%). The aggregates of hydrone on the LDCU caused the dissolution and swelling of nutrients, and then the diffusion of nutrients through the concentration gradient. Conclusions: A though the nutrient release of the LDCUs was affected by many factors, the successful development of the LDCUs will help improve the rapid development of the coated fertilizer industry. [ABSTRACT FROM AUTHOR]