Radish is an important annual root vegetable crop, whose yield is largely dependent on taproot thickening and development. However, the regulatory network of WOXs-mediated taproot development remains poorly understood in radish. Herein, the RsWOX13 was classified in an ancient clade of the WOX gene family that harbors a conserved homeodomain. RT-qPCR analysis revealed that the RsWOX13 gene was highly expressed in radish roots, leaves and flowers. Interestingly, both the promoter activity and expression of the RsWOX13 gene were significantly induced by cytokinin treatment, particularly at 3h. RsWOX13 possessed a transcriptional activation property, that was localized in the nucleus in tobacco leaves. Moreover, overexpression of RsWOX13 resulted in increased plant weight and root width in Arabidopsis, while virus-induced silencing of RsWOX13 inhibited cell expansion and cambium cell activities in radish. Several genes involved in cell wall biogenesis, hormone signaling and sucrose metabolic pathways were differentially expressed in the pTY and RsWOX13-silenced radish plants. Further investigations demonstrated that RsWOX13 directly activated the transcription of RsARR9, RsSUS1a, RsEXPA9 and RsEXPA1 genes by binding to their promoters, indicating that it promoted taproot development by integrating cell division and expansion and sucrose metabolism pathways. These results would provide novel insight into the molecular mechanisms underlying taproot development and facilitate enhancing root yields through genetic engineering approaches in radish.