Vaginal reconstruction is the main solution to the problem of sexuality and gender roles for patients with no vagina. A tissue‐engineered vagina may be the best choice. However, many defects have been found in neovaginas reconstructed with a graft only. In this study, we investigated whether a stem cell‐seeded graft would accelerate the morphological and functional recovery of neovaginas. CM‐DiI‐labeled bone marrow mesenchymal stem cell (MSC)‐seeded small intestinal submucosa (SIS) (SIS+MSCs group) was used for vaginal reconstruction in a rat model; unseeded SIS (SIS group) was used as a control. The neovaginas of each group were harvested at 4 and 12 weeks after surgery. Morphological analyses were performed using hematoxylin and eosin (H&E) staining and immunohistochemical staining for α‐smooth muscle actin (SMA), protein gene product 9.5(PGP9.5), and CD34. Functional recovery was evaluated using an organ bath study. The role of MSCs in the neovagina was analyzed by immunofluorescence and molecular biology methods. At the 4th week, a regenerated epithelium covered the whole neovagina in both groups. A small amount of smooth muscle regeneration was found in the neovagina. Up to the 12th week, nerve fibers appeared. There were more smooth muscle and nerve fibers, along with better contractility, in the neovagina of the SIS+MSCs group. Further study showed that the MSCs differentiated into smooth muscles at the 4th week. A higher microvessel density (MVD) and more vascular endothelial growth factor (VEGF) were found in the neovagina of the SIS+MSCs group. In short, MSCs accelerate the structural and functional recovery of the neovagina.