In this study, the inhibitory mechanism of chlorogenic acid-grafted chitosan (CA-g-CS) against Pseudomonas fluorescens at the gene level were investigated by combining transcriptomics and bioinformatics. Transcriptome results demonstrated that differential expression genes (DEGs) in the CA-g-CS treated group were concentrated in inorganic ion transport metabolism and outer membrane. Protein-protein interaction (PPI) network analysis showed that a large number of significantly down-regulated genes were closely related to iron transport in bacteria. Among them, Tonb-dependent outer membrane protein receptors Fiu, TbpA and FecA of P. fluorescens were significantly down-regulated under CA-g-CS treatment by -5.092, -3.768 and - 3.716 Log