Amu Darya Basin (also known as Karakum Basin) with rich natural gas resources is located in Central Asia. The Jurassic pre-salt carbonate reservoirs (Callovian-Oxfordian) is the main oil and gas producing layer. There are various types of Jurassic pre-salt carbonate gas reservoirs in the right bank block of Amu Darya River, and the gas-water system is complex. The unclear understanding of the reservoir forming process makes it difficult to predict the distribution of natural gas. In recent exploration practice, the discovery of sporadically distributed small reservoirs further shows the non-uniformity of oil, gas and water distribution and the complexity of oil and gas reservoir formation and evolution in this area. Through the analysis of structural evolution and geochemical experiment analysis and by using basin simulation technology, the hydrocarbon generation and expulsion simulations of main source rocks were carried out. Combined with the anatomy of typical oil and gas reservoirs, the evolution of pre-salt carbonate oil and gas reservoirs is restored, and the oil and gas migration and accumulation patterns and the distribution of oil, gas and water are summarized, so as to provide a basis for predicting the favorable enrichment area of oil and gas and for the next exploration deployment. The result shows that: (1) Three sets of source rocks including Lower-Middle Jurassic coal measures, Upper Jurassic marlite and mudstone are developed in the right bank block of Amu Darya River, and there are three types of crude oil, including normal crude oil, low maturity condensate and high maturity condensate. The oil-sources comparative analysis shows that the normal crude oil mainly comes from the mudstone of the Upper Jurassic, and the two types of condensate mainly come from the coal measure source rocks of the Middle and Lower Jurassic, with the characteristics of mixed source. (2) There are two main reservoir forming periods in the right bank block of Amu Darya River: the end of Early Cretaceous-early Late Cretaceous and the end of Late Cretaceous-early Paleogene. The early stage is dominated by the filling of the condensate oil and gas generated by the Lower-Middle Jurassic coal measure source rocks, mixed with some normal crude oil generated by the Upper Jurassic source rocks. The late stage is dominated by the filling of natural gas generated by the Lower-Middle Jurassic coal measure source rocks. (3) The right bank block of Amu Darya River has the characteristics of reservoir formation and evolution of "early oil and late gas, east-west differentiation, differential displacement and adjustment and transformation". The generation and migration of oil and gas in the eastern region occurred earlier, but the trap was formed in Paleogene and shaped in Neogene later, so it mainly preserved late gas. The western region has experienced the filling of oil and gas in the Late Cretaceous and the evolution process of gas displacing oil since Paleogene. The difference of displacement intensity is the main reason for the difference of oil and gas phase state.