Cystatins play an important role in various physiological and pathological processes of organisms, including regulating protein metabolism, antigen processing, inflammatory response, nutritional disorders, and controlling enzyme activity. However, research on immunity functions of fish cystatin M is limited. In this study, Pampus argenteus cystatin M (Pacystatin M) was identified and analyzed. Its amino acid sequence was highly conserved in teleosts, and included the conserved cystatin cysteine protease inhibitor motifs. Pacystatin M was highly expressed in the gill, spleen, and intestine, whereas the expression levels of liver and kidney were lower. Furthermore, Nocardia seriolae infection up-regulated the expression of Pacystatin M in the kidney, spleen and liver, with particularly significant expression observed in the liver on day 15 post-infection. Functional analysis indicated that the recombinant Pacystatin M showed increasing inhibitory activity against papain within a certain concentration range, suggesting that the inhibition was likely competitive. Additionally, Pacystatin M demonstrated the ability to inhibit bacterial growth and high thermal stability. These results suggested that Pacystatin M might be involved in the immune response to microbial invasion and provided new reference addressing disease issues in the large-scale farming of silver pomfret.