It has been reported that mesenchymal stem cells (MSC) derived from adult tissues are effective in promoting wound healing. However, the cell quality varies and cell number is limited as both depend on donations. Moreover, dissociated MSC delivered to an inflammatory lesion are subject to challenges to their survival and functions. Here we demonstrate that dropping of spheres of MSC derived from human embryonic stem cells (EMSC) onto murine dermal wound had much higher survival and efficacy than topical application of dissociated EMSC. RNA sequencing on cells isolated from the wound highlights the CXCL12-CXCR4 signalling in the EMSC sphere-mediated efficacy, which was verified via CXCL12 knockdown in EMSC and CXCR4 inhibition in target cells such as vascular endothelial cells, epithelial keratinocytes, and macrophage. Finally, we enhanced the biosafety of EMSC spheres by engineering the cells with an inducible suicide gene. Together, we propose topical application of EMSC spheres as an unlimited, quality-assured, safety-enhanced, and noninvasive therapy for wound healing and the CXCL12-CXCR4 axis as a key player in the treatment.