Highly ordered mesoporous organosilica thin films containing functional organic terminal groups covalently bonded to the silica matrix were synthesized by co-condensation of tetraethylorthosilicate (TEOS) and organotriethoxysilane RSi(OEt)3 (R = Cl(CH2)3, CN(CH 2)3) in the presence of cetyltrimethylammonium bromide (CTAB) as structure directing agent under acidic conditions. The influence of the nature and concentration of these organic groups on the structure of the thin films is evidenced by Grazing Incidence Small Angle Scattering (GISAXS) and X-ray reflectivity. We show that the introduction of chloropropyl groups strongly affects the structure of these films while cyanopropyl groups weakly perturb it. In the case of the chloropropyl groups, the presence of trans and gauche conformers in the films is clearly evidenced by using micro-Raman spectrometry. Their effects on the phase behaviour versus the concentration are discussed.