To manufacture transparent waterborne polyurethane composite coatings that possess desirable mechanical and flame retardancy properties is still a challenge. Herein, we first synthesized phosphorus-silicon functionalized cellulose nanocrystals (FCNC) filler, and further introduced it into waterborne polyurethane (WPU) matrix to prepare composite. The phosphorus-silicon-containing components were grafted covalently on the surface of FCNC, and the FCNC showed good dispersion level in water and WPU matrix. Moreover, the inserted FCNC could not only maintain the high transparency of WPU-FCNCs composites, but also remarkably enhancing the mechanical and flame retardancy performances. Noticeably, the WPU-FCNC3 composite containing 3 wt% of FCNC showed balanced mechanical (σ b = 16.7 MPa, ε b = 557.5%), limiting oxygen index (22.9%), and a UL-94 rating of V-2 among prepared films. Additionally, WPU-FCNC3 composite exhibited significantly reductions in heat release during combustion, and also showed a high transmittance of 92.2%. The present research supplies promising way for developing transparent, toughness, and flame retardant composite coatings.