Tea polyphenols (TP), as common antioxidants, have been widely used to mitigate for the protection and preservation of aquatic animals, but the protective effect of TP against the deterioration of shrimp muscle quality induced by aflatoxin B1 (AFB1) has not been reported. This study was designed to analyse the root cause of AFB1 induced declines in shrimp muscle quality and the protective mechanisms of TP at the molecular level. Shrimp were exposed to AFB1 and TP for 20 d following a dose-escalating trial, and changes to the muscle histopathology, basic nutrient composition, and protein composition were determined. Non-labelled quantitative proteomics was used to screen and identify differential marker proteins associated with AFB1 and TP. After 20 d of AFB1 exposure, the water content, crude protein content and crude fat content of the shrimp muscle decreased to 68.66%, 18.27% and 1.01%, respectively, while the ash content was positively correlated with AFB1 dose (R2 = 0.955). AFB1 caused damage to the shrimp muscle microstructure in a dose-dependent manner, such as significant enlargement of muscle fibre spaces, rupture of the sarcomere, inflammation and so on. AFB1 induced changes in muscle protein composition, resulting in a decrease in the content of myofibrillar, sarcoplasmic and stroma proteins, while the alkali-soluble protein content increased significantly. TP can effectively protect against the damage to shrimp muscle caused by AFB1 by inhibiting the expansion of muscle fibre spaces and inflammation. TP (0.04–0.16% feed) also had a significant protective effect against the decrease of muscle nutrients and changes in protein composition of shrimp caused by exposure to AFB1 (1.2–2.7 mg/kg feed) in the early and middle period (4–12 d), but the protective effect was weak or not noticeable in the late period (16–20 d). Eleven proteins were identified and screened as biomarker proteins of AFB1 induced quality decline and TP protection, which were involved in energy metabolism (fructose 1,6-bisphosphatase; transaldolase; fructose-bisphosphate aldolase; arginine kinase), redox reaction (hydroxyphenylpyruvate reductase; prostaglandin reductase 1; protein arginine N-methyltransferase 8), anti-inflammatory responses (5′-nucleotidase; actin-depolymerizing factor) and protein translation/folding (eukaryotic translation initiation factor 3; peptidyl-prolyl cis-trans isomerase). This study provides a better understanding of AFB1 induced damage to shrimp quality and technical guidance for the use of TP to prevent the damage during the culture and processing of Penaeus vannamei.