ABSTRACT Background Cementum is a mineralised tissue that is essential for maintaining periodontal tissue homeostasis. Our previous research has shown that dental pulp mesenchymal stem cells (DPSCs) can regenerate periodontal tissues. However, the regeneration efficiency and the specific molecular mechanism remain unclear. Objective This study aimed to clarify the expression differences of the Wnt signalling pathway in cementum, dental pulp and periodontal ligament and illustrate the function of Wnt3a in promoting cementum regeneration of DPSCs. Methods RNA Smart transcriptome sequencing was performed to illustrate the differential gene expression of the Wnt pathway among cementum, dental pulp and periodontal tissues. Biological function experiments of Wnt3a were conducted to demonstrate the capacity of Wnt3a to enhance cementum regeneration of DPSCs. The specific mechanism of Wnt3a function was clarified through single‐cell sequencing and western blotting. Results The expression of the canonical Wnt signalling pathway, especially Wnt3a, was significantly higher in cementum, while DPSCs mainly express the non‐canonical Wnt signalling pathway. Furthermore, Wnt3a could enhance the cementum regeneration of DPSCs in vitro and in vivo. Single‐cell RNA‐seq analysis showed that Wnt3a promoted the cementogenic differentiation of DPSCs via the classical Wnt signalling pathway. Conclusions The results unveiled that the non‐classical Wnt signalling pathway of DPSCs would limit the efficiency of cementum regeneration. Wnt3a could improve the efficacy of DPSCs‐mediated cementum regeneration through activating the canonical Wnt pathway, which may offer a promising therapeutic approach to tooth regeneration.