According to the complex differential accumulation history of deep marine oil and gas in superposition basins, the Lower Paleozoic petroleum system in Tahe Oilfield of Tarim Basin is selected as a typical case, and the process of hydrocarbon generation and expulsion, migration and accumulation, adjustment and transformation of deep oil and gas is restored by means of reservoine-forming dynamics simulation. The thermal evolution history of the Lower Cambrian source rocks in Tahe Oilfield reflects the obvious differences in hydrocarbon generation and expulsion process and intensity in different tectonic zones, which is the main reason controlling the differences in deep oil and gas phases. The complex transport system composed of strike-slip fault and unconformity, etc. controlled early migration and accumulation and late adjustment of deep oil and gas, while the Middle Cambrian gypsum-salt rock in inner carbonate platform prevented vertical migration and accumulation of deep oil and gas, resulting in an obvious “fault-controlled” feature of deep oil and gas, in which the low potential area superimposed by the NE-strike-slip fault zone and deep oil and gas migration was conducive to accumulation, and it is mainly beaded along the strike-slip fault zone in the northeast direction. The dynamic simulation of reservoir formation reveals that the spatio-temporal configuration of “source-fault-fracture-gypsum-preservation” controls the differential accumulation of deep oil and gas in Tahe Oilfield. The Ordovician has experienced the accumulation history of multiple periods of charging, vertical migration and accumulation, and lateral adjustment and transformation, and deep oil and gas have always been in the dynamic equilibrium of migration, accumulation and escape. The statistics of residual oil and gas show that the deep stratum of Tahe Oilfield still has exploration and development potential in the Ordovician Yingshan Formation and Penglaiba Formation, and the Middle and Upper Cambrian ultra-deep stratum has a certain oil and gas resource prospect. This study provides a reference for the dynamic quantitative evaluation of deep oil and gas in the Tarim Basin, and also provides a reference for the study of reservoir formation and evolution in carbonate reservoir of paleo-craton basin.