Objective The purpose of this study was to establish a palatal organ culture method and to investigate the palatogenesis in vitro. Methods 20 pregnant 14-day mice were killed, embryos were separated ascetically, and palatal shelves were dissected and placed on a modified Trowell’s system. All explants were cultured 24 h and 48 h respectively. Finally, all explants were embedded and stained by Hematoxylin and Eosin. Results All explants grew healthy. After incubation for 24 h, medial edge epithelium maintained, whereas after 48 h, medial edge epithelium disappeared, bilateral mesenchymal cells contacted, palates fused. Conclusion This method provides an effective way for investigating the etiology of cleft palate in vitro.