Understanding the types, characteristics, and controlling factors of natural fractures in deep and ultradeep carbonates is crucial for evaluating reservoir quality, optimizing well deployment, and comprehending their impact on hydrocarbon exploitation. Multiple types of natural fractures are widespread in the deep carbonates of the Feixianguan Formation in the Puguang area, northeastern Sichuan Basin, China, and the main controlling factors are complex. Based on geological, geophysical, and experimental data, this study defined fracture types and analyzed the fracture development characteristics in the deep Feixianguan carbonates. On this basis, the main geological factors that control the development and distribution of tectonic fractures were discussed by combining statistical and experimental analyses. Results indicate that natural fractures in the Feixianguan Formation can be genetically classified into tectonic and diagenetic fractures. Specifically, tectonic fractures include shear fractures and tensile fractures, in which the former are predominant. In the Feixianguan carbonates, tectonic shear fractures are mainly developed in the NE-SW and near E-W strikes, with dip angles mostly ranging from 30 to 70°. The majority of shear fractures appear on a small scale and have good effectiveness. The fracture heights and apertures are commonly less than 50 cm and 25 μm, respectively, and unfilled fractures account for more than half. The distribution and development of tectonic fractures are mainly controlled by lithology, mechanical stratigraphy, reservoir physical properties, diagenetic cementation, and faults. In the Feixianguan carbonates, tectonic fractures are more developed in crystalline dolomite. With the increasing thickness of mechanical stratigraphy, the fracture density decreases and the scale increases. The presence of early dissolution pores can prevent the formation of later tectonic fractures. Tectonic fractures in the NNW-SSE and near N-S strikes generally possess poor effectiveness due to multiple cementations after their formation. In the vicinity of faults, tectonic fractures generally stretch subparallel to the extension direction of the fault, and the development degree of fractures close to major faults is higher.