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Significant development has been achieved with bioceramics and biopolymer scaffolds in the construction of artificial bone. In the present study, we have developed and compared chitosan–micro hydroxyapatite (chitosan–mHA) and chitosan–nano hydroxyapatite (chitosan–nHA) scaffolds as bone graft substitutes. The biocompatibility and cell proliferation of the prepared scaffolds were checked with preosteoblast (MC3T3-E1) cells. Total Volume (TV), bone volume (BV), bone surface (BS), trabecular thickness (Tb.Th), trabecular number (Tb.N) and trabecular separation (Tb.Sp) were found to be higher in chitosan–nHA than chitosan–mHA scaffold. Hence, we suggest that chitosan–nHA scaffold could be a promising biomaterial for bone tissue engineering.