The nearly analytic discrete (NAD) method is a kind of finite difference method with advantages of high accuracy and stability. Previous studies have investigated the NAD method for simulating wave propagation in the time-domain. This study applies the NAD method to solving three-dimensional (3D) acoustic wave equations in the frequency-domain. This forward modeling approach is then used as the “engine” for implementing 3D frequency-domain full waveform inversion (FWI). In the numerical modeling experiments, synthetic examples are first given to show the superiority of the NAD method in forward modeling compared with traditional finite difference methods. Synthetic 3D frequency-domain FWI experiments are then carried out to examine the effectiveness of the proposed methods. The inversion results show that the NAD method is more suitable than traditional methods, in terms of computational cost and stability, for 3D frequency-domain FWI, and represents an effective approach for inversion of subsurface model structures.