Green nanocomposites containing biodegradable poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) and cellulose nanocrystals/silver (CNC-Ag) nanohybrids were synthesized and their properties were investigated. It was found that homogeneously dispersed CNC-Ag could act as bifunctional reinforcements to improve the thermal, mechanical and antibacterial properties of PHBV. Compared to pristine PHBV, the tensile strength and the maximum decomposition temperature (Tmax) of the nanocomposite with 10 wt% CNC-Ag were enhanced by 140% and 24.2 °C, respectively. The nanocomposites displayed reduced water uptake and water vapor permeability along with lower migration level in both non-polar and polar simulants compared to the neat biopolymer, which can be related to the increased crystallinity and improved interfacial adhesion. Moreover, the nanocomposites showed strong antibacterial activity against both Gram-negative E. coli and Gram-positive S. aureus. The results of the study indicate that the high performance nanocomposites show great potential applications in the fields of food, beverage packaging and disposable overwrap films.