Abstract: White-leg shrimp (Litopenaeus vannamei) is prone to spoilage and deterioration during storage due to microbial contamination and the action of endogenous enzymes. This study focuses on white-leg shrimp, Stenotrophomonas acidaminiphila (S-1), and myofibrillar protein, the key quality component of shrimp, with the aim of multidimensional exploring the inhibitory effect of the metabolites of Paenibacillus provencensis (PP-2) on S-1 and the effect on myofibrillar protein properties. By using techniques such as non-targeted metabolomics, it aims to explore the preservative effects of the metabolites of Paenibacillus provencensis (PP-2) on white-leg shrimp from multiple dimensions. Using non-targeted metabolomics and other techniques, it was found that there are 20 antibacterial active substances in the metabolites of PP-2. When these metabolites act on S-1, they can change the cell membrane permeability, resulting in the leakage of intracellular proteins and ultimately the death of bacteria, thus achieving antibacterial effects. Compared with the metabolites of Nisin, Kazachstania servazzii (3-D), Saccharomyces cerevisiae (7-C), and Lactobacillus plantarum, at the end of storage, the protein concentration in the group treated with PP-2 metabolites is relatively low, while the sulfhydryl group content and Ca²⁺-ATPase activity are relatively high, and it has the best effect in maintaining the secondary structure of proteins. This study clarifies the antibacterial mechanism of PP-2 metabolites and their effects on the protein characteristics of white -leg shrimp, opening up a new path for the biological preservation technology of white -leg shrimp and providing a theoretical basis for the application of PP-2 metabolites in the field of aquatic product preservation.