In order to analyze the response mechanism of sunflower seedling to drought stress at protein level and promote the discovery of drought-tolerant related genes, PEG6000 was used to simulate drought stress to treat thedrought-tolerant restorer line R5, and proteomic were sequenced to identify differentially expressed proteins. By the proteomic sequencing of 6 sunflower seedlings from stress group and control group, a total of 25,090 peptide fragments and 5,573 proteins were identified, of which 654 proteins were significantly different proteins. Through functional prediction, GO enrichment, KEGG enrichment, pathway enrichment, protein interaction analysis and sub-cellular localization, the expression of protein in sunflower seedlings under drought stress was preliminarily under-stood. The results of this study provided basis for the future study of molecular response mechanism to drought stress of sunflower seedling, and provide genetic resources for improving drought tolerance of sunflower through genetic engineering and the breeding of new sunflower varieties with drought tolerance.