In this study, carbonate-substituted hydroxyapatite (C-HAp) nanorods were synthesised using a dissolution-precipitation reaction on hydroxyapatite (HAp) nanorods based on long-spined sea urchin (Diadema setosum) shells. From the EDS analysis, the Ca/P molar ratio of C-HAp was 1.705, which was very close to the Ca/P of natural bone apatite of 1.71. The FTIR and XRD analyses revealed the AB-type CHAp of the C-HAp nanorods. The TEM showed the rod-like shape of nanosize C-HAp with a high aspect ratio. The antibacterial test against Pseudomonas aeruginosa and Staphylococcus aureus also showed that C-HAp had a high antibacterial activity. The C-HAp/PVA-based scaffolds were fabricated, using a freeze-drying method, for use in alveolar bone tissue engineering applications. There were various scaffolds, with no filler, with microcrystalline cellulose (MCC) filler, and with cellulose nanofibrils (CNF) filler. The physicochemical analysis showed that adding PVA and cellulose caused no chemical decomposition but decreased the scaffold crystallinity, and the lower crystallinity created more dislocations that can help cells proliferate well. The antibacterial activity showed that the CNF induced the higher antibacterial level of the scaffold. According to the SEM results, the micropores of the C-HAp/PVA/CNF can provide a place for cells to grow, and its porosity can promote cell nutrient supply. The macropores of the C-HAp/PVA/CNF were also suitable for cells and new blood vessels. Therefore, the C-HAp/PVA/CNF scaffold was examined for its cytocompatibility using the MTT assay against NIH/3T3 fibroblast cells with a 24 h incubation. The C-HAp/PVA/CNF scaffold showed a high cell viability of 90.36 ± 0.37% at a low scaffold dose of 31.25 μg mL⁻¹. The scaffold could also facilitate NIH/3T3 cells to attach to its surface. The IC₅₀ value had also been estimated to be 2732 μg mL⁻¹.