Fractures are considered an important controlling factor for hydrocarbon accumulation in the pre-salt carbonate reservoirs of the Zanaral Oilfield. They are also a precondition for the high and stable production of oil and gas. Based on core observations and descriptions, systematic sampling analysis, including rock mineral composition analysis, petrographic thin sections, stained thin sections, porosity and permeability, the study about the characteristics and major controlling factors of microfractures and their influence on the reservoir seepage capacity was performed on Wells 2399A and 2092. The results suggest that although there are few macrofractures, microfractures are common in the study area. There are several types of microfractures, principally including micro-tectonic fractures, grain breakage fractures, microstylolites and micro-corrosion fractures. The micro-tectonic fractures, especially those with relatively large apertures are mostly completely filled with calcite. The formation of micro-tectonic fractures is related to calcite-filled macrofractures, but unrelated to bitumen-filled fractures. The distribution of grain breakage fractures, microstylolites and micro-corrosion fractures differs substantially among the various wells and layers. Most of the grain breakage fractures are partially filled with calcite or barren, and the major corrosion fractures are partially filled with calcite. The non-tectonic factors controlling the distribution of microfractures are complicated and variable, and include facies and differential diagenesis. Micro-tectonic fractures formation is promoted by the local enrichment of brittle minerals, small grain size and strong cementation. Grain breakage fractures are dominant in pure limestones with coarse grains and abundant intergranular pores. Microstylolites mainly distribute in tight limestones with more impurities, and fine-grained micro-corrosion fractures are associated to porosity, density, dolomite and acid-insoluble residues contents of the limestones intermediate between those of grain breakage fractures and microstylolites. Dolomite and acid-insoluble residues were probably concentrated by the formation of stylolites. By contrast, low acid-insoluble residue content facilitates the formation of corrosion fractures. Fractures could significantly enhance the seepage capacity of the reservoirs in the study area. The contribution of microfractures to reservoir seepage is given by stylolites, tectonic fractures, corrosion fractures and grain breakage fractures in this order. High degrees of filling of the tectonic fractures greatly affect their seepage capacity.