As a heterogeneous brittle material, coal contains many micro pores and randomly distributed cracks, which are difficult to observe. With the help of industrial CT scanning equipment and three-dimensional image reconstruction technology, the location and distribution characteristics of the main primary fractures which are irregular and concentrated in the coal section can be effectively restored. On this basis, the conventional triaxial compression tests with confining pressures of 1 MPa and 3 MPa were carried out. Furthermore, the original fracture data were imported into the discrete element software to obtain the meso scale parameters consistent with the indoor test stress-strain curve, and then the biaxial compression numerical simulation tests with confining pressure of 0, 1, 3, 5, 7, 9 MPa and loading rate of 0.01, 0.1, 0.2, 0.3, 0.4, 0.5, 0.7, 0.9, 1.0 m/s were carried out for the models with different distribution patterns of original fractures to compare the different confining pressures. The results showed that the compressive strength, elastic modulus, crack growth morphology and other mechanical parameters of the specimen changed with the loading rate. The results showed that the DEM can be used to simulate the mechanical properties of coal under the influence of primary fractures. With the gradual increase of confining pressure, the compressive strength of coal increased exponentially, and the change of elastic modulus was not sensitive. The failure of the specimen was affected by the primary fracture, which was more significant under low confining pressure. With the increase of loading rate, the compressive strength of the sample increased slowly at first, then increased rapidly and tends to be flat. The failure mode of the sample was significantly affected by the primary cracks at low loading rate, and the failure of the sample end was more obvious at high loading rate.