Surfactant-assisted ball milling (SABM) has been shown to be a promising method for preparing rare earth-transition metal (RE-TM) nanoflakes and nanoparticles. In this work, we prepared SmCo5 nanoflakes by SABM at low temperature, and 2-methyl pentane and trioctylamine were specially selected as solvent and surfactant, respectively, due to their low melting points. The effects of milling temperature on the morphology, microstructure and magnetic performance of SmCo5 nanoflakes were investigated systematically. Comparing with the samples milled at room temperature, the SmCo5 nanoflakes prepared at low temperature displayed more homogeneous morphology and lower oxygen content. Remarkably, better crystallinity, better grain alignment and larger remanence ratio were shown in the samples milled at low temperature, which resulted from the distinct microstructure caused by low milling temperature. The differences in structural evolution between the SmCo5 nanoflakes milled at room temperature and low temperature, including the formation of nanocrystalline, grain boundary sliding, grain rotation, et al., were discussed. It was found that lowering the temperature of SABM was a powerful method for the fabrication of RE-TM nanoflakes, which showed better hard magnetic properties and lower oxygen content. This was important for the preparation of high-performance sintered magnets, bonded magnets and nanocomposite magnets.