Microsphere-based therapy is used to allow drug release to treat the critical site through the choice and formulation of variations drug-polymer combinations. They are also used to control the release of insoluble drug by the biodegradability of polymer. Chitosan is one of the candidates for the polymer matrix because their biodegradability and biocompatibility. Recently, we prepared and characterized the inorganic-organic hybrid derived from chitosan and siloxane units. This hybrid showed the excellent biocompatibility for the osteoblastic cells, fibroblastic cells, and nerve cells, etc. In this study, the microspheres were prepared from this hybrid using the microfluidic systems. The biodegradability, drug releasing behavior and cytocompatibility were investigated.