The laser induced periodic surface structures (LIPSS) has been studied for decades. The generation of LIPSS is almost no limitations in the wavelengths and pulse durations, i.e. all of the laser sources from CW to femtosecond laser can be applied. However, the mechanism of LIPSS is still a debatable issue. In this study, we used femtosecond laser to induce periodic surface structures on the high-Tc superconductor YBCO thin films, which are different from simple metals, semiconductors and dielectrics. By adjusting the fluence, number of pulses, incident angles and the polarization of a laser beam, the LIPSS can be clearly generated on the surface of YBCO thin films and the spatial period can be analyzed through a two-dimensional Fourier transformation of the SEM images. The systematical results in this study provide further information for understanding the mechanism of the LIPSS.