The paper presents a fast motion estimation method for video coding using a quad-tree based normalized cross-correlation (NCC) measure, which operates in the frequency domain with the Fast Fourier Transform (FFT) technique. This approach enhances computational efficiency, reduces the number of motion vectors while maintaining video quality, and outperforms traditional block size methods in terms of performance metrics like PSNR and SSIM. Experimental results confirm that the FFT-based NCC algorithm significantly reduces encoding time by over 50% compared to SAD-based methods.