There are still a lot of uncertainty on the process of the Tibetan Plateau uplift and the response of the Yunnan Plateau in the Cenozoic. In order to have a further understanding on the Yunnan Plateau uplift process, we combine the studies on the sedimentary history of the Jianshui basin and other basins and faults in the Yunnan Plateau. We established magnetostratigraphy for the Wanyao (WY) and Qingyunshuiku (QS) fluviolacustrine sections in the northern and middle parts of the Jianshui basin, which indicates eight reverse magnetozones (R1–R8) and seven normal magnetozones (N1–N7), correlating to Chrons C1r.3r through C3n.2r. The strata are constrained to a span from ∼4.77 to ∼1.73Ma, representing an early Pliocene to early Pleistocene age. The accumulation rate of the WY section has accelerated trend, stopping deposit earlier than the QS section. The stratigraphic characteristics of the two sections and their nearby regions indicate the Shiping–Jianshui (SJ) and Xiaojiang faults have already existed and affected the accumulation of the basin at least since the early Pliocene. According to the history of faults activities and the sedimentary strata of basins, we established the geomorphological evolution process of the Yunnan Plateau since the Neogene.