To investigate the effects of waterlogging stress on grain nutritional quality and pod yield, peanut plants were waterlogged for 3 and 6 days at 7, 14, 21, 28, 35, 42, 49, 56 and 63 days after gynophores touched the ground in 2019 and 2020. Results revealed that compared with the control treatment, the oil and starch content in grain increased, while crude protein and soluble sugar content decreased under waterlogging. Waterlogging stress increased the unsaturated fatty acids content but decreased the saturated fatty acids, essential amino acids, non-essential amino acids and total amino acids content. In addition, waterlogging stress decreased the total pod number per plant by 6.78%-49.33%, 100-pod weight by 1.11%-14.08% and 100-grain weight by 1.85%-16.41%, which caused a 34.33%-55.90% reduction in pod yield per plant.After the gynophore touched the ground for 7 days, waterlogging had a greater negative effect on grain nutritional quality, and longer waterlogging duration led to greater yield reduction. In summary, waterlogging stress caused peanut yield reduction and grain quality deterioration.