A novel nano-hydroxyapatite (HA)/chitosan composite scaffold with high porosity was developed. The nano-HA particles were made in situ through a chemical method and dispersed well on the porous scaffold. They bound to the chitosan scaffolds very well. This method prevents the migration of nano-HA particles into surrounding tissues to a certain extent. The morphologies, components, and biocompatibility of the composite scaffolds were investigated. Scanning electron microscopy, porosity measurement, thermogravimetric analysis, X-ray diffraction, X-ray photoelectron spectroscopy, and Fourier transformed infrared spectroscopy were used to analyze the physical and chemical properties of the composite scaffolds. The biocompatibility was assessed by examining the proliferation and morphology of MC 3T3-E1 cells seeded on the scaffolds. The composite scaffolds showed better biocompatibility than pure chitosan scaffolds. The results suggest that the newly developed nano-HA/chitosan composite scaffolds may serve as a good three-dimensional substrate for cell attachment and migration in bone tissue engineering.