Mesoporous silica MCM-41 and SBA-15 were chosen to study the adsorption and release of bulky biomolecule heparin, in order to develop new heparin controlled delivery system and expand the application of mesoporous materials in life science. To explore how the structure of support such as pore size and surface state affects the accommodation and release of heparin, we used decane as swelling agent to enlarge pores of MCM-41, introduced amino groups for improving the biocompatibility of support, and controllably retained templates in the as-synthesized sample. The influence of modification on the structure of samples was investigated by XRD and N(2) adsorption-desorption, whereas their performance of adsorbing and releasing heparin was assessed with that of toluidine blue method. Both enlarged pore and organic modification significantly promoted the adsorption and prolonged the release of heparin in MCM-41, and the release was characterized with a three-stage release model. The mechanism of heparin release from mesoporous material was studied by fitting the release profiles to the theoretical equation. As expected, some mesoporous composites could release heparin in the long term with tuned dosage.