We have investigated the detailed structures of velocity, density and magnetization intensity along a nearly east west profile from Liugou to Dajing across the southern Junggar Basin using the seismic converted wave profiling and joint inversion of gravity and geomagnetic data. Our observations reveal such important interfaces as interface B (the top surface of the folded basement), interface G (the top surface of the crystalline basement), interfaces C-1 and C-2 (interfaces within the crust), and the Moho (the bottom of the crust). Our results indicate that the crust of southern Junggar Basin with a thickness of 45-50 km and the average velocity of similar to 6.3 km/s is mainly composed of an upper crust (including a deposited cover), a middle crust and a lower crust. The top surface of the crystalline basement (G) and the bottom of the crust (Moho) undulate in a same way, indicating an integrated crustal deformation. A series of faults developed in the basin are oriented nearly north-south and cut through the crystalline crust. The faults serve as passageways connecting the crust and upper mantle and are inferred to have formed by north-south compression and east-west extension. We propose that materials from the upper mantle migrate upward into the crust, intrude laterally, and mix up with the crustal materials, producing a crystalline crust in the basin with high velocity, high density and high geomagnetic intensity. Our observations suggest that the southern Junggar Basin bears a single basement layer whose properties have been changed by the exchange of the materials and the energy of the crystalline crust with those from the upper mantle.