Abstract: Addressing the issue of invasion by smooth cordgrass (Spartina alterniflora) in coastal wetland environments, this paper aims to analyze the inhibitory effects of three herbicides　(glufosinate, glyphosate, and haloxyfop)　on the growth and physiological characteristics of the cordgrass, and to explore the underlying molecular mechanisms. Using the pot-grown cordgrass with similar growth states as experimental subjects, these commonly used herbicides were applied individually, followed by measurements of changes in the growth and physiological indicators of the cordgrass. Additionally, the treated leaves of cordgrass were collected for transcriptome sequencing, combined with Kyoto encyclopedia of genes and genomes　(KEGG) functional annotation and differential gene expression analysis, to decipher the growth response and molecular functional alterations of the cordgrass under herbicide stress. The findings show that all three herbicides effectively inhibited the growth of cordgrass, with glyphosate exhibiting a more pronounced inhibitory effect. Specifically, glyphosate treatment led to a marked decline in the growth indicators of cordgrass, accompanied by the identification of 5826 differentially expressed genes (DEGs), including 2290 upregulated genes and 3536 significantly downregulated genes. Further analysis revealed that glyphosate treatment significantly impacted the phenylpropanoid biosynthesis pathway and plant hormone signal transduction pathway, suggesting that these molecular-level changes could be the primary mechanisms underlying effective inhibition of the growth by glyphosate.