Trans-territory perforator flaps are commonly used to reconstruct large defects of the soft tissues. The distal portion of the flap often becomes necrotic, however, as a result of the jeopardised vasculature of choke zone II. The trophic and vascular regenerative properties of bone marrow mesenchymal stem cells (BMSC) seemed to be a promising approach to prevent flaps becoming ischaemic. The purpose of our study is to evaluate the effects of BMSC on the survival of the three-territory perforator flap. The flap model was created based on the deep circumflex iliac vessel in rats. Eighteen rats were distributed, at random, into three groups. Immediately after the flaps were placed, groups were respectively given a single panniculus carnosus injection at choke zone II of either 1×10 (BMSCs), 1×10 (BMSCs) BMSC, or phosphate-buffered saline (PBS). On postoperative day seven, we assessed the gross view of the flap and survival. We also evaluated microvessels by histological examination and angiogenesis-related gene expression by quantitative real-time polymerase chain reaction. After high dosage of BMSC, the flap survival rate, diameter and density of microvessels, vascular endothelial growth factor (VEGF) and platelet endothelial cell adhesion molecule-1 (PECAM-1/CD31) levels were significantly higher in the BMSC treatment group than the control group. We therefore confirmed the positive effects of BMSC on the survival of multi-territory perforator flaps.