Bio-based polyurethane (PU)-coated controlled release fertilizers are attracting a lot of attention; however, generally they have poor properties, so it is difficult for them to meet the agricultural needs. Herein, γ-aminopropyl triethoxy silane (KH550) was first used with nanosilica (NS) to prepare bio-based PU nanocomposite-coated urea (KSPCU). The coating microstructures and nutrient controlled release behaviors of KSPCU were investigated and compared with those of unmodified NS containing PU nanocomposite-coated urea (SPCU) and bio-based PU-coated urea (PCU). The KSPCU with KH550 exhibited an excellent controlled release performance. Its nutrient release longevity exceeded 105 d, which was nearly 6 times greater than that of PCU and 2 times more than that of SPCU, and it was much longer than that of PCU reported in previous research at a coating rate of 3 wt %. A series of characterization methods combined with water resistance capacity and porosity measurements confirmed that a hydrogen bond was formed by the reaction between the nanoparticle and PM200, the nanoparticle was bonded on the macromolecular chain, and KH550 in the coating increased the cross-linking degree, which were beneficial to slowing down the nutrient release of the KSPCU. The innovative application of KH550 on bio-based PU-coated fertilizers will provide a new coating technology for improving their controlled release property.