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Reservoir characteristics and genetic mechanisms of the deeply buried microporous limestones have been determined by integrating mercury injection capillary pressure measurements and scanning electron microscopy (SEM) observations on the Yingshan and Yijianfang formations in the Shunnan area, Tarim Basin. The studied intervals have low porosity (<2%) and permeability (<1 mD). Nearly all the macropores have been destroyed while the micropores, with pore diameters smaller than 10 μm, remain open, even at depths greater than 6,000 m. Based on petrophysical properties, the studied microporous limestones can be grouped into three types. Type I dominated by punctic‐serrate microcrystals is characterized by an intermediate porosity (1.63%), the highest permeability (1.1 mD) and the largest pore‐throat radius (13.01 μm). Type II is highly related with the vast meshed microfabric, which corresponds to the highest porosity of 4.22% but a relatively lower permeability (0.04 mD) and a smaller pore‐throat radius (0.26 μm). Type III mainly consists of the fitted coalescent microfabric and thus corresponds to the lowest reservoir quality (0.33%, 0.005 mD, 0.05 μm). Petrophysical characteristics of these different types are tightly associated with the microcrystals. Micropores hosted between the microcrystals determine the reservoir quality. The depositional textures, by contrast, have no correlation with the reservoir quality. Mudstone may have higher porosity and permeability values than the grainstone cemented by blocky calcite spar. Initial micropores within the limestones are mainly from the dissolution and re‐precipitation progress of the metastable aragonite and high‐Mg calcite. Ostwald ripening effect, which is more significant immediately below the high‐frequency shallowing‐upward sequence, can facilitate the dissolution and re‐precipitation progress, and thus locally improves the reservoir properties dominated by microporosity. Calcite cementation fills nearly all the macropores whereas the micropores remain open. Stylolites in the studied samples behave differently but predominantly act as conduits for fluid flow during the reservoir evolution progress. Since petrophysical properties tend to be independent from depositional textures, it is impractical to link lithology to a specific petrophysical property for the ultra‐deep micropores‐dominated limestone reservoir. [ABSTRACT FROM AUTHOR]