Updated project metadata. Seed longevity is a crucial trait in agriculture as it determines the ability of seeds to maintain viability during dry storage. However, the molecular mechanism underlying seed aging and reduced seed longevity are currently not well understood. Here we report the comparative proteome and metabolome profiling of three rice cultivars varying in aging tolerance including an aging tolerant indica cultivar Dharial, an aging sensitive japonica cultivar Ilmi, and a moderately aging tolerant cultivar A2 that was generated by crossing between Dharial and Ilmi. Results obtained from comparative proteome and metabolome profiling suggest that aged seeds of all the cultivars utilize ubiquitin proteasome-mediated protein degradation which results in the accumulation of free amino acids in Ilmi while tolerant cultivars utilize those for energy production and synthesis of heat shock proteins, especially hsp20/alpha crystallin family protein. Additionally, aging tolerant cultivar seems to activate brassinosteroid signalling and suppress jasmonate signaling to initiate a signaling cascade that allows efficient detoxification of aging induced ROS to maintain the seed longevity during aging. Taken together, these results provide an in-depth understand of aging induced changes in rice seeds.