In ultrasonic non-destructive testing, image reconstruction is essential to restore the diffracted ultrasound signals to improve the lateral resolution of images. Some reconstruction methods, like DAS-based synthetic aperture imaging, are inefficient, especially for reconstructing three-dimensional (3-D) images. Other methods do not provide high-resolution results, because they neglect the distortion effect introduced by transducer geometry. To overcome these disadvantages, we propose a 3-D ultrasonic image reconstruction method based on synthetic aperture wavenumber algorithm. It considers wave diffraction and transducer geometry effects, and can refocus the reflectors even in non-focal zone, which suits for large depth range imaging. This method builds a virtual transducer model in frequency domain by treating the focused transducer as a virtual planar transducer on its focal plane. In addition, the method uses non-uniform fast Fourier transform and deconvolution operation to achieve the 3-D image reconstruction, which has remarkably improved the efficiency and accuracy. According to the experimental results, the lateral resolution of an image reconstructed by the proposed method can reach 290.2 μm, exceeding the lateral resolution limitation of the 15 MHz focused transducer (523.24 μm). Furthermore, the proposed method only takes 0.744 s to reconstruct a 3-D image with 1000×100×100 pixels, while the time domain SAFT takes about 1163.8 s. It shows the potential for real-time 3-D imaging under advanced hardware.