The organic solvent-based nitrocellulose (NC) coatings exhibit a high volatile solvent content, leading to significant environmental pollution. Whereas, existing waterborne NC-based coating have demonstrated poor water resistance and complex application methods. Therefore, this study aims to develop a green and highly water-resistant waterborne NC-based coating system utilizing a simple anti-solvent method with two environmentally friendly plasticizers, namely acetyl tributyl citrate (ATBC) and triethyl citrate (TEC), as film-forming additives. The dynamic light scattering (DLS) studies revealed that the particle size of NC-based nanoparticles increased with an increase in ATBC content, while it remained relatively constant with an increase in TEC content. Moreover, the particle size results demonstrated that the storage stability of aqueous dispersions containing NC/ATBC (NA) was superior to those containing NC/TEC (NT). Additionally, the physicochemical properties of aqueous dispersions-based films (Ndis), including film formation, hygroscopicity, water resistance, transparency, thermal stability, and mechanical properties were evaluated using solvent-based films (Nsol) as control samples. The results demonstrated that the Ndis films exhibited a dense and uniform structure, with physical and chemical properties that were essentially comparable to those of Nsol films. However, the mechanical properties of Ndis films were somewhat influenced by the nanoparticle size, leading to reduced mechanical performance when the particle size of nanoparticles in the aqueous dispersion was excessively large. The equilibrium moisture content for NA and NT films were reduced to 1.119% and 1.872%, respectively, at a relative humidity of 95%, in comparison to pure NC films (3.975%). Simultaneously, water contact angle measurements indicated an increase from 77° for pure NC film to 89° for NA film and 82° for NT film. All films exhibited superior transparency characteristics. Overall, NA films display excellent water resistance and transparency as well as good mechanical properties.