The magnetic films of Co with Si/SiO 2/Pt/Co/molecule structure were fabricated and their structural properties and magnetic anisotropy were investigated by varying both Co (0.5-1.8 nm) thickness and molecular capping layers of 5,6,11,12-tetraphenylnaphthacene (rubrene) and copper phthalocyanine (CuPc), respectively. The crystal structures were characterized using x-ray diffraction (XRD) and the magnetization curves were measured using vibrating sample magnetometer with an applied field both in parallel and perpendicular to a film plane. It was found that the thickness of Co for the maximum perpendicular magnetic anisotropy (PMA) is around 0.7 nm for both group films. However, the estimated effective magnetic anisotropy energy for Co was 2.9 ± 0.3 × 10 6 erg/cc for rubrene-capped sample, which was smaller than the value of 4.9 ± 0.4 × 10 6 erg/cc for CuPc-capped sample. The XRD patterns showed the crystal structure of rubrene layer was of amorphous structure and CuPc layer was polycrystalline. The different interface effects of Co/CuPc and Co/rubrene were discussed to analyze the change of PMA.