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We analyzed 360 permanent and campaign GPS data from 1999 to 2017 in the southern Sichuan-Yunan block, and obtained crustal horizontal deformation in this region. Then, we derived the strain rate using a multi-scale spherical wavelet method. Results reveal a complex pattern of tectonic movement in the southern Sichuan-Yunnan block. Compared to the stable Eurasian plate, the maximum rate of the horizontal deformation in the southern Sichuan-Yunnan block is approximately 22 mm/a. The Xiaojiang fault shows a significantly lower deformation—a left-lateral strike-slip movement of 9.5 mm/a. The Honghe fault clearly shows a complex segmental deformation from the north to south. The northern Honghe fault shows 4.3 mm/a right strike-slip with 6.7 mm/a extension; the southern Honghe fault shows 1.9 mm/a right strike-slip with 1.9 mm/a extension; the junction zone in the Honghe and Lijiang–Xiaojinhe faults shows an obvious clockwise-rotation deformation. The strain calculation results reveal that the maximum shear-strain rate in this region reaches 70 nstrain/a, concentrated around the Xiaojiang fault and at the junction of the Honghe and Lijiang–Xiaojinhe faults. We note that most of the earthquakes with magnitudes of 4 and above that occurred in this region were within the high shear strain-rate zones and the strain rate gradient boundary zone, which indicates that the magnitude of strain accumulation is closely related to the seismic activities. Comparison of the fast shear-wave polarization direction of the upper-crust with the upper-mantle anisotropy and the direction of the surface principal compressive strain rate obtained from the inversion of the GPS data reveals that the direction of the surface principal compressive strain is basically consistent with the fast shear-wave polarization direction of the upper crust anisotropy, but different from the polarization direction of the upper mantle. Our results support the hypothesis that the principal elements of the deformation mechanism in the southern Sichuan-Yunnan block are decoupling between the upper and lower crust and ductile flow in the lower crust.