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Background: Distraction osteogenesis(DO) is a valuable bone regeneration technique, yet its prolonged consolidation phase often entails pain, high costs, infection risks, and lifestyle disruptions. Finding adjunctive approaches to shorten treatment duration is thus of clinical significance. Long noncoding RNAs have been demonstrated to play pivotal roles in regulating bone formation, and homeobox transcript antisense intergenic RNA(HOTAIR) was also reported to regulate osteogenesis and bone formation. However, its role in DO remains unclear. Methods: The effects of HOTAIR on osteogenesis were examined in rat bone marrow-derived mesenchymal stem cells(BMSCs) by asssessing ALP activity, calcification, and osteogenic gene expression with HOTAIR knockdown or overexpression. Using a tibial DO model, HOTAIR-stably silenced BMSCs or control cells were locally injected into the percutaneous distraction gap, and the effects were evaluated by micro-CT, dual-energy X-ray examination, mechanical testing, hematoxylin and eosin staining, and immunohistochemistry. Results: In the present study, it was found that HOTAIR silence promoted while its overexpression suppressed the osteogenic differentiation of BMSCs. The Mechanistic study revealed that HOTAIR physically interacted with FTO, and disrupted FTO ubiquitination and degradation, leading to FTO up-regulation and suppressing osteogenesis. Using DO animal model, HOTAIR-silenced BMSCs stimulated new bone formation and accelerated DO healing in vivo. Conclusion: Silence of HOTAIR enhanced osteogenesis in BMSCs and facilitated DO healing by recruiting FTO and inducing its degradation. Translational potential: The findings generated from this study suggest that inhibitor of HOTAIR may be developed as a promising strategy for DO patients.