The catalytic hydrogenation of fatty acids has witnessed rapid development in recent years. However, the conventional hydrogenation process often requires high-pressure hydrogen. This paper describes a novel protocol to produce fatty alcohols via an in situ hydrogenation of fatty acids in water and methanol using Cu-based catalysts. Cu/ZrO2, Cu/MgO, and Cu/Al2O3 were prepared by the co-precipitation method. All Cu-based catalysts exhibited excellent activity for in situ hydrogenation of fatty acids, and the stability of Cu/ZrO2 was the best. The structures and properties of Cu-based catalysts are demonstrated by transmission electron microscopy, X-ray diffraction, H-2 temperature-programmed reduction, N-2 adsorption-desorption, CO temperature-programmed desorption, and CO2 temperature-programmed desorption. The stability of Cu/ZrO2 is caused by the good hydrothermal stability and tetragonal phase formation of ZrO2, which strongly binds to active Cu. The better activity over Cu/Al2O3 is caused by the larger surface area, higher Cu dispersion, smaller Cu particle size, and strbnger basicity of Cu/Al2O3. Furthermore, the effects of the reaction time, catalyst loading, methanol loading, carbon number, and types of hydrogen donor on in situ hydrogenation of the fatty acids were investigated to demonstrate the reaction behaviors.