In the combined finite-discrete element method, the crack element was an important bridge to realize the transition from continuous to discontinuous deformation. The crack element was assumed as a non-thickness cohesive element, which could not be tested directly. The fracture energy rate for the crack element was an essential parameter determining the deformation and fracture process during the FDEM simulation. However, the common parameter calibration method required experience and time. Thus, a new estimation method of fracture energy rate was derived based on the energy mechanism. The proposed estimation method was consistent with the Griffith fracture criterion but also can reflect the influence of mechanical and inherent properties. Then, the influence of fracture energy rate on rock strength and fracture characteristic was analysed. The results showed that both the tensile strength and uniaxial compressive strength were increased with the fracture energy rate. A smaller tensile fracture energy rate would lead to a larger ratio of tensile fracture and a decrease in shear fracture. It was opposite for the shear fracture energy rate. Based on the rock strength and fracture characteristics, the initial coefficient of fracture energy rate should be 1.0. The fracture energy rate determined by the proposed estimation method and initial coefficient was close to the optimal value, which was well verified by the laboratory test result and tunnel engineering. Finally, the improved calibration steps of fracture energy rate for the complex material were put forward, which was expected for the fast and accurate calibration of model parameters.