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Cellulose nanocrystals (CNC) are natural, renewable, and biocompatible materials that have been widely used as new sustainable reinforcing nanofillers in polymer composites. We present polyvinyl alcohol (PVA)/CNC composites with improved mechanical and antibacterial properties using CNC-based nanofillers. The surface esterified CNC (ECNC) was prepared by 6-bromohexanoyl chloride via surface esterification. Subsequently, the alkyl bromide group of the ECNC was transferred to quaternary ammonium groups for preparing quaternized CNC (ECNC-Qn) by introducing tertiary amino groups with different carbon chain lengths (C8–C16). Then, ECNC-Qn were blended with a PVA matrix to prepare PVA/ECNC-Qn nanocomposite films via a solvent casting procedure. Diverse features, including light transmission, mechanical properties, and antibacterial activity against Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria were investigated. Compared with pure PVA films, the PVA/ECNC-Qn nanocomposite films had higher tensile strength and higher antibacterial activity. Specifically, the maximum tensile strength and elongation at break of PVA/ECNC-Qn nanocomposite films were 45.4 MPa and 318.4%, respectively, which were 37.2% and 94.3% higher than those of pure PVA film, respectively. Moreover, the ECNC-Q8 exhibited the highest antibacterial efficiency, leading to the best antibacterial activity for PVA/ECNC-Q8 nanocomposite films among all films. This study demonstrates an efficient method for preparing a functional, environment-friendly PVA composite film. The prepared PVA/ECNC-Qn nanocomposite films exhibited considerable application potential in the packaging field, owing to their good mechanical and antibacterial barrier properties.