In order to evaluate the potential petroleum system within the Meso-Neoproterozoic strata of the southwest North China Craton (NCC), we explored the deep-buried basal tectonics on the Precambrian basement and the residual sedimentary thickness of the Meso-Neoproterozoic in the Ordos Basin. A combination of geophysical processing methodologies has been conducted. Based on regional seismic exploration, the shallow gravity effects caused by the undulation of the Cenozoic, Jurassic, Carboniferous and Cambrian sedimentary formations were calculated through forward modeling, and eliminated the free-air gravity anomaly by a gravity stripping technique. Subsequently, by using the wavelet multi-scale decomposition method, the deeper gravity effect sourcing from underneath the Meso-Neoproterozoic base was calculated and then eliminated, including the undulation of Paleoproterozoic-Archaean crystalline basement and the lateral density discontinuity of the lower crust. As a result, the residual gravity anomalies caused by the Meso-Neoproterozoic sedimentary formations and the Moho discontinuity of the Ordos Block were both obtained, which was then used for inversion. The inversion results show that the residual Meso-Neoproterozoic strata are mainly distributed in the southwest and northern part of the Ordos Block, and the Moho depth of the Ordos Block averages about 42 km. It ranges from 38 to 42 km in the eastern part and deepens to over 44 km in the west. In addition, there are some detailed deep-structure reflections on the Moho discontinuity. For instance, the parallel-arranged NE-trending anomalous belts in southwest Ordos Block indicate strong crustal extension and mantle uplift. The regional geology indicates that the NE-trending crustal extension is not related to the Cenozoic strike-slip pull-apart process around the Ordos Block, nor the Indosinian Movement in Early Mesozoic, or the cratonic depression in the Paleozoic. However, it highly resembles the NE-oriented paleo-rifts that developed in the Meso-Neoproterozic aulacogens. The residual crustal gravity anomaly eliminates both the shallow disturbance from the sediments and the deep shadow from the mantle. It shows very good consistency with the undulation of the Meso-Neoproterozoic sedimentary basement along a classical interpreted seismic survey line, which validates the correlation between the NE-trending anomalous belts with the basal aulacogen tectonics. According to seismic interpretation, the paleo-rifts within the Precambrian aulacogens occurred during the Mesoproterozoic and continued into the early Neoproterozoic. Huge volumes of sediment filled the rift troughs during the Meso-Neoproterozoic, causing a significant gravity loss on the gravity field, and formed considerable oil–gas exploration potential. Given suitable paleoclimatic conditions, the grabens would have provided a favorable environment for organic-rich shales and source rocks to develop. While the faults controlling the grabens and horsts would have played an important role in the migration and accumulation of hydrocarbons in the potential petroleum system. Combined with paleoclimate and lithofacies paleogeography analysis, five favorable areas are speculated for Meso-Neoproterozoic potential petroleum systems, which are the northwest Yimeng Uplift, the northern Tianhuan Depression, the southern Tianhuan Depression, the southwestern to central Yishaan Slope and the western Weibei Uplift, respectively. Based on lithofacies paleogeography, source rock maturity and organic carbon abundance, it suggests that the favorable petroleum systems within the Proterozoic strata of the Ordos Block were obviously controlled or influenced by the deep paleo-rifts and block faults, which resulted in forming three types of play, called the Weathering Model, the Tilting Model and the Transition Model. In particular, the central to western parts of the Yimeng Uplift and the southern Tianhuan Depression, where the Weathering Model developed, as the Upper Paleozoic coal-bearing source rocks have large hydrocarbon generation potential and good preservation conditions, these two areas should be regarded as important favorable prospecting regions in the Ordos Basin.