To analyze the effects of drought treatments on physiological indexes and DNA methylation levels of Brassica Rapa， this study subjected oilseed rape Longyou 7 to three treatments， namely， normal water supply， drought stress， and rehydration after drought， followed by analyzing the physiological indexes and DNA methylation after treatments. In comparison to those under normal water supply treatment， the oilseed rape under drought stress exhibited 167.27%， 254.85%， 103.24%， and 164.64% of increase on malondialdehyde content， SOD， POD and CAT activities， respectively. Osmoregulatory substances Pro and SP were elevated up to 3.21 μg/g and 0.048 μg/mg， respectively； the relative water content of leaves decreased significantly by 53.64%. The physiological indexes decreased partially after rewatering. Compared with normal water supply treatment， the methylation level showed an increasing trend after drought， while the methylation rate after rewatering was even higher than that of drought and control， with the methylation rate reaching 20.56%. Through GO enrichment analysis， differentially methylated genes （DMGs） were enriched in biological processes， nucleus， and molecular functions. KEGG functional enrichment analysis showed that DMGs were mainly involved in the ubiquitin mediated protein hydrolysis， cytotoxicity， ABC transporter proteins， carbon fixation in photosynthetic organisms， and other metabolism-related pathways. A correlation between methylation rate and physiological indicators was observed， and through integration of both GO and KEGG enrichment results， seven DMGs were revealed encoding peroxidases. The results of this study will provide a basis for unrevealing the regulatory mechanism to drought stress in rapeseed and breeding for drought tolerant new varieties.