The application of chitosan in packaging has always been limited due to its brittle and hygroscopic nature. In this study, hydrophobic short-chain fatty acids (SCFAs) were utilized to modify chitosan to overcome this issue. For the first time, hydrophobic SCFAs, typically hexanoic acid and its homologs, were found to be able to dissolve chitosan in water as well as its hydrophilic analog. After water was removed through evaporation, hydrophobic SCFA-modified chitosan films were obtained. The results of mechanical testing and DSC analysis confirmed that these hydrophobic SCFAs could effectively plasticize the chitosan film. Moreover, water contact angle measurements revealed that the hydrophilicity of these plasticized chitosan films was significantly reduced. The findings from the moisture uptake experiments indicated that linear hydrophobic SCFAs reduced the hygroscopicity of the chitosan film. Additionally, the crystal structures, thermal and gas barrier properties, and antibacterial activities of these hydrophobic SCFA-modified films were systematically examined and compared with those of hydrophilic SCFA-modified chitosan. This study presents an innovative and practical method for modifying chitosan films by regulating the structure of the cosolvent, thereby facilitating the real-world application of chitosan-based food packaging materials.