Biopolymers have shown great application prospects due to their advantages of being biodegradable, renewable, non-toxic, safe and inexpensive. However, the innate hydrophilicity of biopolymers means the materials prepared from them easily swell or disintegrate in aqueous media, limiting their applications. Herein, on the basis of improving the mechanical performance of a sodium alginate/poly(vinyl alcohol) (SA/PVA) film by introducing palygorskite (Pal) nanorods, the hydrophobicity of the obtained SA/PVA/Pal film was improved further by surface coating with methyltrichlorosilane (MTCS) through a vapor deposition-surface polycondensation reaction. MTCS nanofilaments, with a size of approximately 50 nm, were formed on the film surface by the silanization reaction between MTCS and hydroxyls, resulting in an improvement in surface hydrophobicity characterized by a contact angle (111.8°) higher than that of SA/PVA/Pal film (72.7°). Therefore, the obtained films maintained their original shape and strength after soaking for a long time in aqueous solutions containing acid, alkaline, and electrolyte, also in organics, while the uncoated film dissolved quickly and lost its original shape. Moreover, the surface coating also increased the film's tensile strength from 11.43 to 28.69 MPa. This demonstrates a simple, universal and effective way to improve the resistance of biopolymer-derived materials to water and various chemicals.