Laser shock peening (LSP) with nanosecond or femtosecond laser pulses is applied to improve the mechanical properties of metallic materials. Thus, it is necessary to compare the effects of different processing methods on microstructure changes and property improvement. In this study, nanosecond LSP (NLSP), femtosecond LSP (FLSP), and LSP with combined nanosecond and femtosecond laser pulses (F-NLSP) are conducted on Ti6Al4V alloys to compare the surface morphologies, in-depth microstructures, and nanohardness changes. In FLSP, the peened surface is smooth, and the affected depth is limited near the peened surface. NLSPed and F-NLSPed samples present rough surfaces due to the severe ablation process. Small equiaxed grains with no preferred grain orientation are denser in F-NLSPed samples than that in NLSPed samples. Compared with NLSPed samples, the affected depth and amplitude of in-depth nanohardness are larger in F-NLSPed samples. This is attributed to the increased laser absorption of incident laser on the treated surface by femtosecond laser pulses. The results in this study show the effects of different LSP methods and provide chances in engineering potentials for material property improvements.