Tertiary is the final stage of the wide continental sedimentary in Sichuan Basin, and also the important tectonic deformation period. To analyze the sedimentary-filling pattern and the tectonic evolution characteristic of the prototype basin is significant to reveal the evolution of the Sichuan Basin forming process, and it is the key to restore the paleogeography and paleoclimate of the Sichuan Basin. In this paper, from the viewpoint of basin-mountain combination, we reconstructed the structure-paleogeographic pattern, analyzed the sedimentation-filling characteristics and restored sedimentary facies belt distribution characteristics in different periods on the basis of seismic, drilling, outcrops and various geological data. Obviously controlled by the tectonic load derived from the adjacent orogenic thrust and preexistent tectonic blocks in the basin basement, the sedimentary region limited to the southwestern, southern of Sichuan Basin and mainly composed of fluvial and lacustrine facies sedimentary environment with the process of continuous compressing, sediment filling, trend to shrink and ultimately disappears in Late Tertiary. The remnants of tertiary strata consisting of Mingshan, Lushan and Dayi conglomerate formations from the bottom up. Experienced several depositional stages including: Firstly, with alluvial fan and desert sediment on the edge of the lake duo to the tectonic load derived from the adjacent orogenic thrust and the warm and dry climate, with fast deposition at the stage of the Mingshan Formation; Secondly, is characterized by sand shale interbed and in the process of continuous shrink and the tectonic activity is relatively stable at the stage of the Lushan Formation; Finally, alluvial fan deposition developed along strike from SW to NE at the stage of the Dayi conglomerate stage. The southwestern Sichuan Basin has been demonstrated to be a typical intercontinental depression basin in the Tertiary Period in accordance with tectonic and sedimentary evolutions. The factors such as tectonic activity and climate change played an important role in the formation and evolution of the prototype basin, at the same time, it is deeply affected the paleogeographic and the rule of the sedimentation-filling pattern in Tertiary.