—Deep and ultradeep oil and gas have been the prominent direction of international exploration in recent years. The deep oil and gas resources are predominantly distributed in the three domains of carbonate, clastic, and igneous rocks. The carbonate rock reservoirs contain about 40% of global oil and gas reserves owing to their superior reservoir properties. In recent years, a number of large oil and gas fields have been discovered in the deep marine carbonate rocks in China, especially in the Sichuan and Tarim Basins, thus showing a vast oil and gas exploration potential in these rocks. In this paper, the genesis and source of deep natural gas in the Tarim and Sichuan Basins were systematically studied. The results show that the natural gas in the deep marine carbonate rock reservoirs is generated not only from the later deep-source rocks. Also, the substantial cracking of crude oil and pyrobitumen in the reservoir under conditions of great burial depth and high geotemperature can provide abundant natural gas sources for the deep reservoir. So, the contribution of gas from oil cracking should be considered in evaluation of deep natural gas resources.