Cancellous bovine bone scaffold, as a temporary 3-D framework, initiates human extracellular matrix morphology with a porosity of 50-90%, pore size of 100-1000 μm, and is heterogeneous and anisotropic. Researchers have developed various conventional techniques to form better morphology. The Cell and Tissue Bank of RSUD Dr. Soetomo developed Deproteinized Bovine Bone Material (DBBM) from local bovine bone by thermal deproteinization, heated to 1000°C, leaving only inorganic components that are hard to degrade. Freeze-Dried Bovine Bone (FDBB) is produced through lyophilization, retaining organic components that are potentially immunogenic, thus requiring further decellularization (DC-FDBB) using Sodium Dodecyl Sulphate (SDS) to remove these components and increase porosity, while still maintaining extracellular matrix structure. Previous studies have not presented complete data on the morphology of these materials. Aim: The study aims to compare the morphology of FDBB, DC-FDBB, and DBBM scaffolds. Material and Methods: Five cube-shaped of FDBB, DC-FDBB, and DBBM group were observed for porosity, pore size, trabecular thickness, number of trabeculae, degree of anisotropy, connectivity density, bone surface density, and structure model index using Micro CT. Comparative analysis using ANOVA test was subsequently carried out to evaluate the differences in these variables among the groups. Results: FDBB and DBBM differed significantly in porosity (p = 0.002), pore size (p = 0.004), degree of anisotropy (p = 0.008), and structure model index (p = 0.008) with Post Hoc Tukey HSD. FDBB and DC-FDBB significantly differed in porosity only (p = 0.031). DC-FDBB and DBBM significantly differed in connectivity density (p = 0.020) and structure model index (p = 0.002). Conclusion: The most ideal microarchitecture morphology were DBBM and the least were DC-FDBB.