Granular soil generally exhibits an anisotropic stiffness in engineering but challenging to quantify in situ and laboratory condition, due to a lack of the appropriate factor and quantitative research. In this paper, discrete element method is employed to create two typical types of soil fabric and conduct shear wave measurement in double direction, with the microscopic parameters monitored to investigate the connection with macroscopic stiffness anisotropy. The results show that the reference fabric increases as fabric anisotropy increases first and then decreases with further increase in the XZ stress plane, while always decreases approximately linearly in the XY stress plane. The reference fabric is determined by the contact density in the direction of wave propagation and particle perturbation under microscale examination. The results also reveal a linear relationship between the macroscopic stiffness anisotropy and microscopic fabric anisotropy, which could be used as an effective method to reflect the degree of anisotropy in situ by wave measurement. And the applicability of the expression of small-strain shear modulus is also discussed.