In this study, two kinds of polyimides were prepared to investigate the effects of molecular structures on the properties of corresponding waveguides. Three kinds of the diamines were used for investigating the polarizability of the bridge group on the C-H band length and their overtone bands, including 4,4’-oxydianiline (ODA), 4,4’-thiodianiline (TDA), and 4,4’-diaminodiphenylmethane (DPM). It was found that the stronger the electron-withdrawing group of the diamines moiety of the polyimides, the shorter the C-H bond length on the aromatic ring. Thus, the C-H overtone band shifted to a lower wavelength and reduced the corresponding optical loss. Therefore, the order of the normalized optical loss was PMDA/ODA > PMDA/TDA > PMDA/DPM. Photopatternable polyimides with the 3-aminopropyltriethoxysilane (APrTEOS) and methacrylic acid-2-dimethylaminoethyl ether (MDAE) as the end capping and photosensitive moieties were successfully prepared. The retardation of the film shrinkage by incorporating the silica moiety was successfully achieved. The present studies were usefully for design and processing of polymer based channel waveguides.