The Binchuan Basin in northwest Yunnan, SW China, is a rift basin developed at the intersection of the Red River Fault and Chenghai Fault, where active faults developed and historical earthquakes occurred. Understanding the fine velocity structure of the shallow crust in this region is crucial for comprehending earthquake occurrences and mechanisms and for improving earthquake location accuracy. Using the continuous waveform data recorded by 381 dense array stations in 2017, we obtained 7915 Rayleigh-wave phase velocity dispersion curves in the period band of 0.2-6 s from ambient noise cross-correlation functions after rigorous data processing and quality control. We determined 3-D isotropic and azimuthally anisotropic shear wave velocity models at depths above 6 km in the shallow crust based on the direct surface wave azimuthal anisotropic tomography method. The isotropic model reveals a strong correspondence between the S-wave velocity structure at depths of 0-1 km and the regional topography and lithology. The Binchuan depocenter, Zhoucheng depocenter, Xiangyun Basin, and Xihai Rift Basin are primarily composed of Quaternary deposits, which show low-velocity anomalies, while the regions with the Paleozoic shale, limestone, and basalt exhibit high-velocity anomalies. The nearly N-S orientation of fast directions from azimuthal anisotropy models are mainly controlled by the active Binchuan Fault with N-S strike as well as the NNW oriented primary compressive stress.