Fish and fishery products are important parts of the human diet, but the microbial, chemical, and physical deteriorations limit their shelf life. Using the modified atmospheric packaging system and edible coatings is one of the main procedures to improve the shelf life of fish. In this research, the effect of chitosan nanoparticles (CNPs) loaded with fennel essential oils along with modified atmosphere packaging (MAP) system on chemical, microbial, and sensorial properties of Huso huso fish fillets during storage at fridge were evaluated. The results showed that coating fish fillets with CNPs and fennel EO significantly reduced the peroxide value, total volatile nitrogen, and thiobarbituric acid value compared with the control samples. Microbial analyses showed a lower number of mesophilic, psychotropic, pseudomonas, and lactic acid bacteria in coated fillets compared with control and MAP packaging. Fish fillets coated with CNPs and EO showed high acceptability in all sensorial attribute through the storage. It can be concluded that using CNPs and fennel EO along with MAP packaging can enhance the shelf life for H. huso fillets up to 18 days in the fridge.