Background: Environmental concerns about petroleum-based plastic packaging materials and the growing demand for food have inspired researchers and the food industry to develop food packaging with better food preservation and biodegradability. Nanocomposites consisting of nanofillers, and synthetic/biopolymers can be applied to improve the physiochemical and antimicrobial properties and sustainability of food packaging. Scope and approach: This review summarized the recent advances in nanofiller and their applications in improved food packaging systems (e.g., nanoclay, carbon nanotubes), active food packaging (e.g., silver nanoparticles (Ag NPs), zinc oxide nanoparticles (ZnO NPs)), intelligent food packaging, and degradable packaging (e.g., titanium dioxide nanoparticles (e.g., TiO2 NPs)). Additionally, the migration processes and related assessment methods for nanofillers were considered, as well as the use of nanofillers to reduce migration. The potential cytotoxicity and ecotoxicity of nanofillers were also reviewed. Key findings: The incorporation of nanofillers may increase Young’s modulus (YM) while decreasing the elongation at break (EAB) (y = −1.55x + 1.38, R2 = 0.128, r = −0.358, p = 0.018) and decreasing the water vapor (WVP) and oxygen permeability (OP) (y = 0.30x − 0.57, R2 = 0.039, r = 0.197, p = 0.065). Meanwhile, the addition of metal-based NPs could also extend the shelf-life of food products by lowering lipid oxidation by an average of approx. 350.74% and weight loss by approx. 28.39% during the longest storage period, and significantly increasing antibacterial efficacy against S. aureus compared to the neat polymer films (p = 0.034). Moreover, the migration process of nanofillers may be negligible but still requires further research. Additionally, the ecotoxicity of nanofillers is unclear, as the final distribution of nanocomposites in the environment is unknown. Conclusions: Nanotechnology helps to overcome the challenges associated with traditional packaging materials. Strong regulatory frameworks and safety standards are needed to ensure the appropriate use of nanocomposites. There is also a need to explore how to realize the economic and technical requirements for large-scale implementation of nanocomposite technologies.