Porous hydroxyapatite (HA) scaffolds combined with a drug delivery system have attracted much attention for bone tissue engineering. In this study, an easy and highly efficient method was developed to immobilize salvianolic acid B (Sal B)-loaded chitosan (CS) microspheres three dimensionally and homogeneously on the surface of HA scaffolds pre-coated with alginate. Porous HA scaffolds were prepared via a template-leaching process and CS microspheres (used as drug carriers) were fabricated by an emulsion method. To improve adhesion between the microspheres and HA scaffolds, alginate was used to pre-coat the porous surface of the HA scaffolds. Various concentrations of alginate were used to optimize the adhesion of Sal B-loaded CS microspheres to the scaffold surface. During the adherence process, coated HA scaffolds were immersed in an aqueous solution containing Sal B-loaded CS microspheres, followed by standing or shaking at 37 °C for a certain time. The results showed that the microspheres were solidly and homogeneously distributed on the porous surface of the alginate pre-coated HA scaffolds via electrostatic interactions. Few microspheres detached from the porous surface, even after the HA scaffolds with microspheres were treated by shaking in distilled water for as long as 7 d. Compared with the static condition, the distribution of Sal B-loaded CS microspheres on the porous surface of pre-coated HA scaffolds in the shaken condition was more homogeneous and almost unaggregated. Additionally, the compressive strength of the scaffolds coated with alginate was obviously improved. The optimal alginate coating concentration was 1% (i.e. the microstructure of the porous surfaces of the HA scaffolds was almost unchanged). The release profile of Sal B over a 30 d immersion found an initial burst release followed by a sustained release. The result of cell culture in vitro was that 1% alginate-coated scaffolds with Sal B-loaded CS microspheres obviously promoted cell proliferation after cell culture for 3 and 7 d, and cells were attached and uniformly distributed on the porous surface of the scaffolds. The strategy of incorporating drug-loaded microspheres with porous HA scaffolds could provide an excellent bone substitute for repair of bone tissue defects.