Understanding the fracture mechanism of concrete is very important for the safety design of concrete structures. We develop a 3D discrete element model with softening effect to study the fracture behaviors of quasi-brittle materials. The basic ideas of our model inspired from the flat-joint concept and the cohesive crack model are implemented in the framework of MUSEN, which is an open source discrete element software with CPU–GPU accelerating computation. The placement-package-compaction method is proposed together with laser scanning technology to construct the meso-scale geometric model of concrete. The meso-parameters of 3D discrete element model developed are calibrated by uniaxial compression and splitting tension tests of concrete. The validation of the present model is verified by the laboratory test of concrete. Compared with the results predicted by the flat-joint model, the F-CMOD curves and fracture parameters simulated by our model are in good agreement with that of the laboratory tests of concrete. Finally, it is concluded that the fracture strain of bond significantly affects the fracture behavior but the softening mode does not. It is found that the linear one is better choice among three softening modes in the present model.