Regenerative medicine through the application of tissue engineering and cell transplantation has provided a new door for wound healing. In this study, the healing effect of human Wharton's jelly stem cells (WJSCs) labeled with superparamagnetic iron oxide nanoparticles (SPIONs) seeded onto polyvinyl alcohol/chitosan/carbon nanotubes (PVA/CS/CNTs) in burn wounds was investigated by performing magnetic resonance imaging (MRI) and Prussian blue staining. Human WJSCs were prepared from umbilical cord and characterized. PVA/CS/CNTs were fabricated via electrospinning. Forty-eight rats were divided into four groups. The control group underwent a third-degree burn injury and was left untreated. The second group received silver sulfadiazine after burn induction, the third group was treated with PVA/CS/CNTs after burn wounds, and the fourth group received WJSCs labeled with SPIONs seeded onto PVA/CS/CNTs following burn injury. Tensile strength was investigated, real-time polymerase chain reaction was used to evaluate apoptosis, and Prussian blue staining and MRI were performed to trace labeled cells. The mesenchymal properties of WJSCs were characterized. Histologically, healing was observed as complete granulation occurred and epithelial tissues were formed in the absence of inflammatory cells, with increased expression of Bcl-2 and a decrease in Bax genes in the fourth group. Internalization of SPIONs within WJSCs was confirmed by Prussian blue staining and MRI on day 14. WJSCs labeled with SPIONs seeded onto PVA/CS/CNTs could successfully participate in the healing of burn wounds and could be easily tracked by MRI as a noninvasive method, providing a new door in regenerative medicine for burn wounds.