The objective of this research was to explore the antimicrobial activity and mechanism of carvacrol against Vibrio Parahemolyticus, Shewanella putrefaciens, Staphylococcus aureus and Pseudomonas fluorescens and evaluate the effect of the addition of carvacrol/β-cyclodextrin emulsions to flaxseed gum (FSG)-sodium alginate (SA) edible films on the preservation of Chinese sea bass (Lateolabrax maculatus) fillets during refrigerated storage. The minimum inhibitory concentration (MIC) of carvacrol against V. parahemolyticus, S. putrefaciens, S. aureus and P. fluorescens were 0.5, 0.5, 0.125, and 0.5 mg/mL, respectively. Alkaline phosphatase activity assay, nucleotide and protein leakage, and scanning electron microscope demonstrated that carvacrol damaged the external structure of the tested bacterial cells causing leakage of cytoplasmic components. At the same time, when FSG-SA films containing carvacrol used as coating agents for Chinese sea bass fillets cold storage, FSG-SA films containing 1.0 or 2.0 mg/mL carvacrol could significantly reduce TVB-N content, K-value, the degree of microbial deterioration and maintain quality of sea bass fillets according to organoleptic evaluation results.