The Taiyuan Formation limestone gas reservoir in Ordos Basin is an important replacement area for gas accumulation and upper production, in which the bioclastic beach and biohummocks microfacies are favorable reservoir facies zones of the Taiyuan Formation limestone. In the process of fracturing, it is found that these two types of limestone develop structural high-angle fractures and have the conditions to form a complex fracture network of volume fracturing. To support the optimization process of fracturing and determine the influence law of natural fractures on the deformation and failure of bioclastic beach and biohummocks limestone, triaxial compression experiments were carried out under confining pressures of 0, 10, 20, 30, 40, 50 and 60 MPa, and the weak surface strength theory of biohummocks limestone was established. The results show that dilatancy and natural fracture shear slip are the important deformation and fracture mechanisms of the Taiyuan Formation limestone under confining pressure, and obvious shear zones occur in the bioclastic beach limestone when the confining pressure is greater than 50 MPa. The mechanical properties of natural fractures in the bioclastic beach are stronger than that of the matrix, which has a strengthening effect on the mechanical properties of limestone. The mechanical properties of natural fractures in biohummocks are weaker than that of the matrix, which has a weakening effect on the mechanical properties of limestone. Based on the weak surface strength theory, natural fractures with angles between 50° and 80° have activation potential in biohummocks limestone reservoirs. This study provides a theoretical basis for reforming limestone reservoir of Taiyuan Formation.