To fabricate and characterize the porous hydroxyapatite-based scaffold, honeycomb as a natural polymer (HA/HCB) and paraffin wax (HA/Wax) were used. The fabrication of scaffold using the porogen leaching method was varied temperatures between 700, 900, and 1100 degrees C. Theoretically, the temperature of calcination influenced the morphology of the scaffold, crystallite size, functional group, and porosity. According to the previous study, the crystallite size of the polymer scaffold is less than 100 nm. The HA-based scaffold was analyzed by the Energy Dispersive X-Ray Spectroscopy (EDS), Scanning Electron Microscopy (SEM), X-Ray Diffractometer (XRD), Fourier Transform Infrared Spectroscopy (FTIR), and tested by the cell viability. According to the XRD results, the crystallite size of HA/HCB scaffold decreases, while scaffold HA/Wax crystallite size tends to decrease when calcination temperature increases. As calcination temperature increases, porosity tends to be small for both HA/HCB and HA/wax scaffolds. The scaffold HA/HCB 900 degrees C has interconnected pores, uniform, and small porosity. In contrast, the scaffold HA/Wax 900 degrees C has fewer interconnected pores and non-uniform particles. The FTIR result of the HA/HCB 900 degrees C has C-H functional group, affecting cell viability. Through MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5 diphenyltetrazolium bromide) assays, the cell viability value of the HA/Wax 900 degrees C was greater than the HA/HCB 900 degrees C for 48 h incubated time. It is caused by the alkane chains on HA/HCB, causing the death of cells. Considering cell viability assay studies for the nanocomposite scaffold, the obtained results confirm the non-toxicity of the material.