Inedible natural oils are desired resources for renewable fuel and chemical production. Herein, a nonprecious metal cobalt catalytic system was developed for selectively hydrogenating fatty acids and natural oil into fatty alcohols or long chain alkanes. The cobalt-based catalysts were prepared by a wet-impregnation method with a series of supports including HZSM-5, CeO2, ZrO2, SiO2, Al2O3, TiO2, and hydroxyapatite (HAP) for hydrogenating stearic acid. Among these catalysts, Co/HAP exhibited the highest activity and 97.1% yield of 1-octadecanol was obtained at 190 degrees C and 4 MPa H-2 in water. Additionally, the Co/HAP was capable of directly hydrogenating the natural oil, Jatropha oil, to fatty alcohols without any preprocessing, and 83.1 wt % yield of alcohols could be achieved at 190 degrees C and 4 MPa H-2 in water. Co/HAP could also catalyze the complete conversion of stearic acid and Jatropha oil to long-chain alkanes when dodecane was used as solvent. X-ray power diffraction, transmission electron microscopy, H-2 temperature-programmed reduction, and NH3 temperature-programmed desorption were carried out, and the high catalytic activity of Co/HAP could be due to its desired acidity, cobalt particle dispersion, and stronger metal support interaction. The Fourier transform infrared results indicated that the high efficiency of Co/HAP could also be due to the absorption of fatty acid on the surface of catalyst which thus promoted the hydrogenation process over Co species. The possible reaction pathway was also proposed according to the conversion process tracking of stearic acid.