Protein-oxidized soybean meal (OS) is soybean meal whose proteins have undergone oxidative damage during storage, causing oxidative stress and inflammatory injury in animals. Quercetin (Q) has been shown to possess antioxidant and anti-inflammatory effects. Therefore, to explore these effects of Q on rats fed OS, a 2 × 2 two-factor completely randomized design was adopted. 48 SD rats were randomly divided into four groups: fresh soybean meal (FS) group, FS + Q group, OS group, and OS + Q group, and fed for 28 days. The results showed that compared with the FS diet, the OS diet significantly increased serum levels of glucose and urea nitrogen (P < 0.05), and induced inflammatory lesions in the duodenum, jejunum, and liver. The OS diet reduced total antioxidant capacity (T-AOC), glutathione peroxidase (GSH-Px) activity while increasing reactive oxygen species (ROS) content in the jejunum (P < 0.05); In the liver, it increased malondialdehyde (MDA) content but decreased glutathione (GSH) levels and GSH-Px activity (P < 0.05); the OS diet elevated the contents of the IgG and interleukin-6 (IL-6) in both jejunum and liver (P < 0.05), and up-regulated jejunal and hepatic pathways related to heme biosynthesis and ROS synthesis (P < 0.05). In contrast, compared with the diet without Q, Q supplementation significantly reduced serum globulin levels (P < 0.05), and improved intestinal and liver inflammatory lesions. In the jejunum, Q supplementation decreased ROS content and increased catalase (CAT) activity and T-AOC (P < 0.05), and downregulated the “heme biosynthesis” pathway (P < 0.05); In the liver, it increased T-AOC and decreased MDA content (P < 0.05), down-regulated the “ROS metabolic process” and related molecular pathways (P < 0.05), and normalized the expression of key genes (Ccl20, Duox1, Cyp4a2) and proteins (Ccl20, Duox1) in jejunum and liver (P < 0.05). These findings indicate that Q alleviates OS-induced oxidative stress, inflammation, and tissue damage in rats by regulating heme and ROS pathways.