Three kinds of carboxymethyl chitosan/β-cyclodextrin microspheres loaded with theophylline were prepared by spray drying intended for pulmonary delivery. Mucociliotoxicity, permeation rate, and drug release characteristics of the product were investigated. The microspheres obtained by spray drying were found to be spherical with smooth or wrinkled surfaces. The mean particle size was between 3.39 and 6.06 μm. The microspheres demonstrated high product yield (43.7-50.2%), high drug loading (13.7-38.1%), and high encapsulation efficiency (86.9-92.8%). FT-IR indicated that there were interactions of theophylline with carboxymethyl chitosan matrix. Further studies on mucociliotoxicity and permeation confirmed that microspheres had better adaptability and high permeation rate. In vitro drug release from the microspheres was not related to the drug/polymer ratios.