Chilling stress inhibits the taproot yield in radish ( Raphanus sativus L.), but the molecular and genetic mechanism underlying taproot growth under chilling stress is largely unknown. In this study, the transcriptome variation between leaf and taproot of radish under chilling stress was explored. Transcriptome analysis of chilling stress and taproot development revealed that the transcription level of RsDREB2B was upregulated with the growth of taproot and suppressed by long-term chilling treatment. It was revealed with RT-qPCR that RsDREB2B expression was rapidly accumulated within 12 h after chilling treatment. Overexpression of RsDREB2B significantly enhanced the chilling tolerance of Arabidopsis and radish plants, and also effectively promoted the elongation of hypocotyl and root length in Arabidopsis. Yeast one-hybrid (Y1H) and dual-luciferase reporter assays (DLA) indicated that cold-related genes ( RsCORs: RsCOR15A and RsCOR413PM1) were activated by RsDREB2B, while the RsDREB2B expression was inhibited by RsCDF3. The expression of RsCDF3 was increased after long-term chilling treatment, and the RsCDF3-OE plants exhibited a decrease in the root elongation. Taken together, it was revealed that RsDREB2B modulated chilling tolerance through triggering the expression RsCORs, and chilling stress inhibited taproot growth via RsCDF3- RsDREB2B module in radish. These findings uncovered a vital role of RsDREB2B in regulating the taproot growth under chilling stress in radish, which would facilitate engineering chilling-tolerant cultivars in radish and other root vegetable crops.