In clinical dentistry practice, supplemental bone surgery or jawbone defect after tooth extraction must be assisted by a bone-filling material. Cobalt-substituted hydroxyapatite (COHA) effectively promotes bone cell growth, reduces the inflammatory response, and is an antibacterial agent. COHA can therefore be used as an alveolar bone-filling material or guided bone regeneration membrane. Meanwhile, COHA can be used in magnetic resonance imaging (MRI) with negative contrast agents and targeting materials without causing metal interference with the image. Hence, COHA has received increasing amounts of attention in recent years. However, the influence of different cobalt precursors on the synthesized COHA is still unknown. Therefore, COHA synthesized from 3 cobalt precursors (cobalt chloride, cobalt nitrate, and cobalt sulfate) was compared in this study. The results show that COHA synthesized by the precursor with the smallest anion radius, cobalt chloride, has a larger particle size (239 nm) and a higher cobalt ion substitution rate (15.6%). When the cobalt ion substitution rate increases, the MRI has a stronger contrast. Bioactivity data indicate that COHAC is more susceptible to degradation and therefore releases more cobalt ions to contribute to the differentiation of bone cells. Based on these studies, COHAC prepared with the cobalt chloride precursor has a higher cobalt ion substitution rate, faster degradation rate, better image contrast, and better bioactivity. It is therefore the preferred choice of bone-filling material for alveolar bone regeneration.