Wnt signaling, canonical or non-canonical, plays conserved roles in numerous physiological and pathological processes. However, it is well beyond the scope of this review to cover all functional aspects of Wnt signaling in different contexts at reasonable depth; therefore this review intends to cover only the roles of Wnt signaling in bone biology; more specifically, we intend to first update the roles of Wnt signaling in physiological bone process, including in osteogenesis and chondrogenesis, since recent years have witnessed tremendous progressions in this area, and then we seek to extend our understanding to the pathological bone process, especially to the heterotopic ossification (HO), even though the understanding of Wnt signaling in HO has been limited. We then further clarify the potential crosstalking between Wnt and other conserved signaling pathways, including FGF, GPCR and Hif1α pathways. Overall, our goal is to update the progressions, identify the general theme and the knowledge gaps and discuss the potential promising avenue for future applications in HO prevention and treatment.