Diversified characteristics and anisotropism of marine carbonate reservoirs result in the fact that the controlling factors of hydrocarbon accumulation zones are different from that of the clastic rocks in the traditional nonmarine basin. Hydrocarbon accumulation in carbonate is not simply controlled by the secondary structural zone. Analysis of discovered carbonate reservoirs in the Tarim basin shows that development of the reservoirs is controlled by the weathering leaching process of atmosphere freshwater, sedimentation, many types of diagenesis, alteration of deeply fluid. According to the genetic type and the lateral distribution characteristics of reservoirs, the hydrocarbon accumulation zones in the Tarim basin are divided into four types: unconformity and paleoweathering crust, organic buildup reef-bank, inner dolomite, and deep fluid alteration type. Different types of carbonate hydrocarbon accumulation zones are mainly distributed in different parts of many paleouplifts, such as the Tabei uplift, Tazhong uplift, Bachu fault uplift. Because of different genetic mechanisms of reservoirs in different hydrocarbon accumulation zones of carbonate, the reservoir space, reservoir capability, hydrocarbon reservoir type and their distribution are different in general.