Prometryn, a type of herbicide with high efficiency and low toxicity, is used to remove algae in agricultural weeding and aquaculture, as well as in rivers, and reservoirs. Shrimp, sea cucumber, and shellfish are widely used in aquaculture. Prometryn is frequently detected in domestic and foreign marine environments and export marine products, causing ecological risks to fishery breeding environments and affecting the quality and safety of aquatic products. Mactra veneriformis is a common economic shellfish on the coast of China. Owing to its fixed growth position, the risk of net pollution by prometryn is relatively higher. Prometryn can cause changes in the antioxidant enzyme system of marine organisms, thereby affecting their immune mechanisms. Changes in the activity or content of its components can be used as biomarkers of oxidative stress. At present, domestic and foreign studies on prometryn in shellfish primarily focus on the investigation of local contamination and acute toxicity, and the effects on the antioxidant enzyme system and tissue cells of M. veneriformis have not been reported. To investigate the toxicological effect of prometryn stress on M. veneriformis, the 21-day stress and 15-day net water release experiments of different concentrations of prometryn (0.2 μg/L, 1.0 μg/L, 10 μg/L) on M. veneriformis were carried out. The activities of superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) in gills and digestive glands at different time points were determined, and the morphological changes of gills tissues were observed. Results showed that prometryn had certain induction or inhibition on SOD, CAT, and GPx in M. veneriformis. Moreover, 0.2-μg/L prometryn had less oxidative stress than that of the 1.0-μg/L and 10.0-μg/L groups. The enzyme activity of the 1.0-μg/L and 10.0-μg/L groups could not be restored entirely or even lost in the water purification release stage. Additionally, the 10.0-μg/L prometryn had irreversible oxidative damage to M. veneriformis. Prometryn could cause atrophy of gill epithelial cells, shedding of cilia, and enlargement of gill filament space. With the increase of prometryn concentration or the prolongation of stress time, there were significant SOD, CAT, and changes of gill tissue cells concentration and time effects. Furthermore, high concentrations of prometryn had considerable toxic effects on M. veneriformis. GPx in gills of M. veneriformis can be used as a potential biomarker for assessing prometryn pollution and providing an early warning for marine ecological environment pollution.