Chitosan and N,N,N-trimethyl chitosan (TMC) were treated with heparin (HP) to produce polyelectrolyte complexes (PECs). The structures of PECs were characterized by Fourier transform infrared and CP-MAS 13C NMR spectroscopies. A thermal stability of TMC/HP complex was evaluated by thermogravimetric analyses, and morphology was investigated by SEM images. The ratio between the carbons bonded to noncharged nitrogen atoms (CΦ) and the carbons bonded to positively charged nitrogen atoms (Cω) in TMC was calculated through of the degree quaternization (DQ), being the DQ obtained through 1H NMR data. Experiments of controlled release of HP were performed in distilled water at pH ∼7, using methylene blue/heparin system as solute. The release profiles of HP from TMC/HP complex are quite different each other. The value of CΦ/Cω ratio was used for explaining such an effect. The CΦ/Cω ratio tends to be constantly (∼0.69) as high as the pH of medium in which the PEC of TMC/HP was obtained. The change of CΦ/Cω ratio on the pH was also considered to explain the improvement of thermal stability of PEC2 with increase of pH. Data show that PEC of TMC/HP formed at pH 8 is a promising material for uses in oral site-specific HP release systems.