This study aimed to elucidate the regulatory mechanisms underlying the toxic effects of glyphosate (GLY) on rainbow clam (M. iridescens), with implications for their culture and conservation. GLY residues in aquatic systems raise significant environmental and public health concerns, yet the underlying mechanisms remain largely elusive. In this study, M. iridescens were acutely exposed to GLY at various concentrations (0, 2.34, 5.45, 12.74, 29.74, and 69.46 mg/L) for 7 days. Gill and hepatopancreas samples were collected to assess oxidative stress status and histopathological examination. Additionally, three concentration groups low concentration (LC) group at 2.34 mg/L, medium concentration (MC) group at 12.74 mg/L, and high concentration (HC) group at 69.46 mg/L were selected for metabolomic analysis. The findings indicated that GLY exposure led to oxidative stress and structural changes in tissues. The metabolomic analysis suggested that GLY exposure exacerbates inflammatory responses and disrupts endocrine function, and sex hormones.