Micro-relief lines were formed on the surface of 45# steel by photonic crystal fiber femtosecond laser with a repetition rate of 50 MHz and 1 MHz respectively. The heights and the widths of the micro-relief lines were affected by the input laser power, the laser scanning velocity and the pulse repetition rate. The specific structure of the micro-relief can be controlled by properly adjusting these parameters. The mechanism for the formation of the micro-relief was also analyzed preliminarily. The heat accumulation of the high repetition rate femtosecond laser induces the surface melting of the 45# steel, which results in the micro-relief structures by the combination of the liquid surface-tension and the temperature gradient.