The recent discovery of Meso-Neoproterozoic primary oil and gas reservoirs within ancient cratonic basins of the world has promoted studies on the mechanism and exploration of these primary reservoirs. The formation and distribution of oil and gas resources are controlled by the tectonic setting, paleogeography, paleo-environment and biological evolutionary history related to supercontinents. The nature and distribution of proto-type basins are a key to oil and gas exploration and evaluation for the Meso-Neoproterozoic basins. This special issue is focused on the theme of “Supercontinental breakup process, basin formation, late deformation, and oil and gas accumulation”. It aims to provide a cross section of the interdisciplinary methods adopted to study Meso-Neoproterozoic basin-forming tectonic settings and evolutionary processes in the three cratons of China, to unravel the tectonic reworking and formation of proto-basins, to reconstruct the tectonic paleogeography and prototype basin, and to identify the effect of the late superimposed geological events for the proto-type basins and their oil and gas petroleum systems.