Abstract Based on seismic data, outcrop evidence, logging data and regional aeromagnetic data, the distribution of Nanhua–Sinian rifts in the southwestern Tarim Basin was analyzed, and on the basis of restoration of lithofacies paleogeography in different periods of Neoproterozoic–Cambrian, the evolution model of the proto-type rift basin was discussed. The Neoproterozoic Rodinia supercontinent split event formed the trigeminal rift system at the edge and inside of the craton in the southwestern Tarim Basin located in the Kunlun piedmont and Maigaiti slope. The rift in Kunlun piedmont zone was distributed along the E-W direction and was the oceanic rift in the trigeminal rift system. Two decadent rifts in N-E strike developed in the Luonan and Yubei areas of Maigaiti slope, and the interior of the rifts were characterized by a composite graben-horst structure composed of multiple grabens and horsts. The Neoproterozoic–Cambrian proto-type basin evolution in the southwestern Tarim Basin can be divided into three stages: rift in the Nanhua, embryonic passive continental margin in the Sinian, and stable passive continental margin in the Cambrian. Despite the regional tectonic movements in the end of Nanhua and Sinian, the tectonic framework of the southwestern Tarim Basin had not changed significantly, the sedimentary center of Nanhua rift basin showed the characteristics of succession in the Sinian–Early Cambrian. The Nanhua rift in Kunlun piedmont evolved into a craton marginal depression during the Sinian–Early Paleozoic, while the Luonan decadent rift in the midsection of Maigaiti slope evolved into a sag inside platform in Early Cambrian, constituting the paleogeographic framework of “two paleouplifts and one sag” with the paleouplifts in east and west sides of the slope. The later evolution of the Luonan decadent rift in the midsection of the Maigaiti slope formed two sets of reservoir-forming assemblages, the Sinian and the Lower Cambrian ones, which are important exploration targets in future.