In order to study the effects of HDACs (histone deacetylation) in winter rapeseed(Brassica rapa L.) under low temperature stress, with strong cold resistance varieties of ‘Longyou 7’, low temperature resistance varieties of ‘Tianyou 4’ and weak cold resistance varieties of Lenox, winter rapeseed as materials, we analyzed HDACs inhibitor trichostatin A (TSA) postpartum seed germination, low temperature stress antioxidant enzyme activity and osmotic adjustment substances content changes, and identified the genetic family of HDACs in the genome and analyzed its expression characteristics in different cold winter rapeseed varieties. The results show that: (1) both 1 and 3 μmol/L TSA have inhibit effect on the root length of three varieties, and the exogenous spray TSA at different temperatures increased antioxidant enzyme activities and osmotic adjustment substance contents. (2) In this study, a total of 21 HDACs members in winter rapeseed were identified, system development result showed that HDACs were divided into three subfamilies, the chromosome location found that all gene were distributed unevenly on eight chromosomes, with no gene distribution on chromosomes 7 and 8. The HDACs promoter sequence contains many cisacting elements that related to stress response, light response and hormones response. (3) The results of different tissue sites showed that most genes were significantly higher in shoot apical meristem than in other tissues. BrapaHDA19, BrapaHDA61, BrapaHDA8 and BrapaHDA72 were high in winter rapeseed, BrapaHDA52 ‘Tianyou 4’ stem leaf, silique, basal leaf (new) and basal leaf (old) have higher expression, and BrapaHDA72 is high in lenox flowers. (4) Low temperature stress expression results showed that BrapaHDA8, BrapaHDA14, BrapaHDA2, BrapaHDT22 and BrapaHDA151 showed differentially expressed in three cold resistance different materials. Inference by the above results, these genes may play an important role in the growth and cold resistance in winter rapeseed.