To alleviate the quality deterioration and extend the shelf life of crucian carp fillets, a bio-based active composite film integrating eugenol (EG)-loaded mesoporous silica nanoparticles (MSNs) modified with caffeic acid (CA) within the zein matrix (EG/CA-MSN/Zein) was developed. This study compared the effects of EG/CA-MSN/Zein, polyethylene (PE), and zein films on the quality of fish fillets during refrigerated storage. The results showed that the EG/CA-MSN/Zein film significantly retarded the increase in pH and microbial growth. Moreover, the film had higher water-holding capacity (WHC), better texture, and color stability, as indicated by low-field nuclear magnetic resonance (LF-NMR), magnetic resonance imaging (MRI), and sensory evaluation. The EG/CA-MSN/Zein composite film extended the shelf life of crucian carp fillets by 3–4 days, highlighting its potential as an environmentally friendly and efficient packaging material for aquatic products.