Femtosecond laser surface modification has been proved to be a versatile technology to create various functional materials by modifying solid surface properties. An interesting experimental phenomenon is found by exposing a Ti6Al4V alloy and Ti-based metallic glass to femtosecond laser irradiation. The research results show that the femtosecond laser induces different micro-nano structures on the surfaces of Ti6Al4V alloy and Ti-based metallic glass. Spherical structure and LIPSS (Laser-induced periodic surface structures) can be formed on the surface of Ti6Al4V alloy after femtosecond laser irradiation. On the surface of Ti-based metallic glass, LIPSS, SWPSS (Super-wavelength periodic surface structure) and neatly arranged microholes structures can be found. Under the same laser parameters, the micro-nano structures showed different evolution trends on the Ti6Al4V alloy and Ti-based metallic glass surfaces. The difference in surface structure between Ti6Al4V alloy and Ti-based metallic glass is since amorphous materials have no crystal lattice and a fixed melting temperature. In addition, there are differences in the biocompatibility of different surface structures. The size and distance of the micro-pits on the surface of different structures determine the ability of cells to adhesion, proliferate and differentiate. This conclusion has important significance for the application of Ti6Al4V alloy and Ti-based metallic glass in the field of biomedicine.