The Fengcheng Formation of the Mahu Sag is an unconventional reservoir that is of paramount importance for exploration and development of hydrocarbon resource. However, current research on natural fractures in the Fengcheng Formation remains limited, posing challenges for exploration of hydrocarbon resource in the region. This study is based on core observations, thin section identification, geochemical testing and the evolution of regional tectonic movements to investigate the characteristics and periods of formation of natural fractures to address this gap. According to the characteristics of natural fractures in the drilling core samples and microsections, the natural fractures in the Fengcheng Formation can be grouped into structural fractures and atectonic fractures. Structural fractures can be further divided into three subtypes: high-angle interlayer shear fractures, along-layer shear fractures, and tensile fractures. Additionally, non-tectonic fractures in this studied area are primarily bedding fractures, hydraulic fractures, and hydrocarbon-generating overpressure fractures. Vertically, fracture development is more prominent at the bottom of Feng #2 Formation and at the top of Feng #3 Formation. Results also indicate that natural fractures primarily formed during three distinct tectonic movement periods. The initial stage of fracture evolution pertains to the Late Permian period (243–266 Ma), filled with fibrous calcite, and exhibiting a uniform temperature of 70–100 °C. The second stage of fracture evolution occurred during the Late Indosinian to Early Yanshanian period (181–208 Ma), mostly filled or semi-filled with calcite, with a uniform temperature of 110–130 °C. The third stage of fracture development happened during the late Yanshanian to early Himalaya period (50–87 Ma), predominantly filled with calcite, and presenting a uniform temperature of 130–150 °C. Among the various types of structural fractures, the density of high-angle interlayer shear fractures demonstrates a positive correlation with daily gas production, indicating their vital role in promoting hydrocarbon resource production and transportation. Furthermore, microfractures generated by hydrocarbon-generating overpressure fractures exhibit small pore sizes and strong connectivity. These microfractures can create an effective permeability system by connecting previously isolated micropores in shale reservoirs, thus establishing interconnected pore spaces in the shale formation.