Selenium-rich rice has become one of the effective ways to increase people’s selenium intake. Selenium-containing proteins have higher antioxidant properties, which may lead to selenium-rich brown rice (Se-BR) having better storage stability than ordinary brown rice (BR). By measuring the peroxidation value, fatty acid value, carbonyl value and protein secondary structure, it was found that Se-BR had higher oxidation resistance stability than BR. The biological function of the differential proteins (DEPs) between ordinary brown rice stored for 0 days (BR-0) and 180 days (BR-6) as well as Se-rich brown rice stored for 0 days (Se-0) and 180 days (Se-6) was investigated by using iTRAQ. A total of 237, 235, 113 and 213 DEPs were identified from group A (BR-0/BR-6), group B (Se-0/Se-6), group C (BR-0/Se-0) and group D (BR-6/Se-6), respectively. Kyoto Encyclopedia of Genes and Genomes analysis showed that the DEPs were mainly enriched in glucose metabolism, tricarboxylic acid cycle, fatty acid biosynthesis and degradation, glutathione metabolism, sulfur metabolism, peroxisome and other metabolic pathways. This study provides theoretical support for the study of protein oxidation kinetics and storage quality control of brown rice during storage.