The study on Meso–Neoproterozoic petroleum systems has attracted extensive attention. However, it still faces some problems such as the availability of hydrocarbon accumulating elements, complexity of accumulation process, and limited petroleum geology data. This study focuses on the Mesoproterozoic petroleum system in the Ordos Basin. By analyzing hydrocarbon accumulation factors, the hydrocarbon migration simulation at the migration and accumulation system scale is integrated into the source rocks evolution simulation at the petroleum system scale. The evolution of the Mesoproterozoic petroleum system was reconstructed using profile and plan views of multi-critical periods. The hydrocarbon migration process of each hydrocarbon accumulation unit was analyzed by hydrocarbon accumulation dynamics, and the simulation results of the hydrocarbon accumulation during each period were superimposed in a single stratum according to its sequence and spatial position to examine the type of each hydrocarbon accumulation and the regularities of the oil–gas distribution. Finally, a methodology comprising five figures and one table was developed to characterize the Mesoproterozoic petroleum system and assess prospective areas. The results of this study are as follows. (1) The plan view and profile of multi-critical periods indicate that the distribution of the Central Paleohigh controlled the hydrocarbon migration and accumulation in the Triassic–Early Cretaceous, during which the oil–gas reservoirs were primarily distributed within the paleohigh and its adjacent region, and oil and gas readjustment and re-accumulation have occurred along the unconformity towards the northeastern region on a large scale since the Late Cretaceous. (2) Integration of the regional geologic setting and some petroleum geology data suggests that in the Changcheng System, the structural highs and unconformity-related traps are of crucial importance for current oil exploration, and the Cambrian weathering crust in the southwestern part of the basin contains abundant oil–gas shows, highlighting the contribution of the Mesoproterozoic petroleum system.