To obtain accurate stress intensity factors (SIFs) with arbitrarily shaped finite element mesh arrangements across the crack front, a modified three-dimensional virtual crack closure technique (modified 3D-VCCT) is proposed in this paper. This method is based on three-dimensional virtual crack closure technique (3D-VCCT) and finite element method. To increase the SIFs calculation accuracy for the crack with arbitrary shape, the length and shape of finite element meshes across the crack front are considered in this method. Then the SIFs with arbitrarily shaped finite element mesh arrangements across the crack front are calculated by three different methods, the modified 3D-VCCT in this paper, the extension of virtual crack closure-integral method proposed by Okada and the 3D-VCCT. The solutions of SIFs obtained by three methods are compared and the comparison results show the modified 3D-VCCT has better accuracy with arbitrarily shaped finite element mesh arrangements across the crack front. In addition, the simulations of fatigue crack growth are carried out by using the modified 3D-VCCT. Then the simulation results are compared with the test results, which shows good agreement.