The arrival times of the converted P-to-S phase at an intra-crustal discontinuity (Pis) or the Moho (Pms) provide a powerful diagnostic tool for detecting anisotropy with horizontal symmetry axis. In this study, we used Pis and Pms arrival times on P receiver functions to determine the anisotropy of the crust from the seismic data recorded by 285 temporary broadband stations and 3 permanent stations deployed in the southeast margin of Tibet. First we measured the splitting parameters of the upper crust by fitting the Pis phase arrival, and then we adjusted the Pms phase arrival to obtain the splitting parameters of the lower crust after correcting for the effect of the anisotropic upper crust on the Pms arrivals. So, we achieved 75 double-layer splitting measurements. In the upper crust the splitting times vary between 0.05 s and 1.34 s with an average of 0.53 s ± 0.29 s, while in the lower crust they range from 0.06 s to 1.42 s with an average of 0.62 s ± 0.33 s. The results confirm that the crust is remarkably anisotropic in the southeastern margin of Tibet. In the upper crust, the fast wave polarization directions clearly show a clockwise rotation around the Eastern Himalayan Syntax, suggesting that the extensional fluid-saturated microcracks induced by rigid extrusion from central Tibet are mostly responsible for the observed anisotropy. In contrast, the lattice preferred orientation of anisotropic minerals induced by a channel flow is the main contributor to the lower crust anisotropy.