Abstract: The Sichuan-Yunnan Block is located on the southeastern margin of the Qinghai-Xizang Plateau and has frequent seismic activity on the western border, posing a potential threat to human society and economic development. Therefore, it is important to understand its geological evolution, assess earthquake risks, and formulate scientific and reasonable disaster prevention and mitigation strategies. Using 23 months of continuous ambient noise records from 81 seismic stations, we obtained 1248 phase-velocity dispersion curves of the fundamental Rayleigh wave at 5–50 s. The three-dimensional (3D) S-wave velocity structure in the northwestern Sichuan-Yunnan Block was obtained by pure-path and depth inversion. The results show that three low-velocity anomalous bands were distributed nearly north-to-south (N-S) at depths of 10–35 km. The overall shape of the low-velocity channel gradually shifted from southeast to southwest because of the influence of the Panzhihua high-velocity blocks. The low-velocity strip consists of three branches, with the first branch extending southwest from the northern part of the Lancangjiang Fault. The second branch is distributed in the N-S direction and is blocked by two high-velocity bodies near the Longpan-Qiaohou and Honghe faults. The third branch crosses the research area from N-S and gradually extends from southeast to southwest and from shallow to deep. The three low-velocity anomaly distribution areas are likely the most severely deformed areas of the collision between the Qinghai-Xizang Plateau and Yangtze Block. The results provide a more detailed understanding of the deep structure of the western boundary of the Sichuan-Yunnan Block crustal low-velocity anomalies and reliable geophysical evidence for the morphology and continuity of crustal flows.