A large bone defect is defined as a defect that exceeds the regenerative capacity of the bone. Nowadays, autologous bone grafting is still the gold standard treatment. In this study, a hybrid bone tissue engineering scaffold (BTE) was designed with biocompatibility, biodegradability and adequate mechanical strength as the primary objectives. Chitosan (CS) is a biocompatible and biodegradable polymer that can be used in a wide range of applications in bone tissue engineering. Hydroxyapatite (HAp) and fluorapatite (FAp) have the potential to improve the mechanical properties of CS. In the present work, different volumes of acetic acid (AA) and different ratios of HAp and FAp scaffolds were prepared and UV cross-linked to form a 3D structure. The properties of the scaffolds were characterised by scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy, swelling studies and compression testing. The cytotoxicity result was obtained by the MTT assay. The degradation rate was tested by weight loss after the scaffold was immersed in SBF. The results showed that a crosslinked structure was formed and that bonding occurred between different materials within the scaffold. Additionally, the scaffolds not only provided sufficient mechanical strength but were also cytocompatibility, depending on their composition. The scaffolds were degraded gradually within a 6-to-8-week testing period, which closely matches bone regeneration rates, indicating their potential in the BTE field.