We conduct a high-resolution seismic tomography for the crustal P and S-wave velocities of Yunnan region in southwestern China. Waveforms recorded at 128 broadband stations from 131 regional earthquakes of moment magnitudes 3.9−5.5 occurring between 2009 and 2021 are used to obtain traveltime residuals by the cross-correlation between records and synthetics. Using the regional community velocity model SWChinaCVM‐1.0 as the initial model, we carry out a three-stage iterative adjoint tomography, progressing from the longer period band of 50–20 s to shorter-period bands of 30–10 s and 30–5 s. The final model shows general consistency in the spatial patterns of P- and S-wave velocity anomalies. Widespread low-velocity anomalies with high-Vp/Vs ratios in the mid and lower crust in the region suggest a mix of weak materials of the mid-lower crustal flow from under the Tibetan Plateau with hot materials of the upwelling from the deep mantle plume that led to the Emeishan Large Igneous Province. Localized velocity and Vp/Vs ratio anomalies also reveal that the Lijiang-Xiaojinhe Fault Zone appears to be confined in the upper crust, while the Anninghe-Zemuhe Fault Zone and the Xiaojiang Fault Zone are both whole-crust structures reaching the Moho interface. The Red River Fault Zone, a whole-crust fault, separates the Yangtze Craton to the northeast from the Indo-China Block to the southwest. The main fault zones, the decoupling between the crustal and uppermost mantle parts, and the wide-spreading weak mid-lower crustal materials mutually interact, all contributing to the tectonic evolution of the entire region.