The chitosan (CHS) chondroitin sulfate (CS) complex microcapsules were prepared by emulsion-chemical crosslink method, with the chitosan and chondroitin sulfate as the wall materials and the low molecular weight heparin (LMWH) as the core materials. The microcapsules were characterized by Fourier transform infrared (IR) spectrometry, scanning electron microscope (SEM), size distribution and thermal analysis. The in vitro drug release behavior of the microcapsules was studied by spectrophotometry. The SEM and size distribution showed that the microcapsules were in the spherical form mostly in the size range of 20-80 microm. The IR spectrum indicated that there were electrostatic interactions between chitosan and chondroitin sulfate, with the sulfate group and free carboxyl group reacted with the amino groups of chitosan. The DSC result showed that the wall materials could protect the core materials of the microcapsules. The results of the release kinetics experiments of the microcapsules showed that the drug released slightly faster in acid media than in alkali ones.