In traditional numerical methods, pre-defined crack paths are often assumed and flow effects of fluids are often simplified as equivalent pressure loads on the crack when modelling hydraulic fracture, which makes it difficult to reflect the coupling effects of seepage and fracture. In this study, a highly efficient Python code was developed to insert pore pressure cohesive interface elements into the solid finite element mesh, and the coupling mechanism of seepage-fracture was considered to model the complicated hydraulic fracture process in quasi-brittle materials. The effectiveness of the model was validated by the simulations of the classic theoretical model and experimental results. Furthermore, the whole process of hydraulic fracture with multiple pre-existing cracks was simulated, the meso-scale hydraulic fracture model of concrete was established, and the influences of aggregates, interface transition zone and permeability of matrix were analyzed. Results show that the developed model can reliably simulate complicated hydraulic fracture problems of quasi-brittle materials, the multi-crack propagation is accompanied by the bifurcation propagation of micro cracks rather than smooth crack propagation trajectory. The aggregates and interface transition zone affect the fracture trajectory, and the bifurcation of crack is generated. The permeability of concrete matrix affects its resistance of hydraulic fracture and failure softening process.