Nitrogen-vacancy color centers (NVs) in diamond have several potential applications ranging from quantum computing to data storage. However, artificial NVs are often close to the surface, which limits their spatial density and applicability. Here we demonstrate an effective and precise method for preparing deep single NVs in diamond. The method is based on a spatial-shaped femtosecond laser to overcome laser defocus in high-refractive materials, and realizes the preparation of single NVs at 95 µm. In addition, owing to the good energy distribution of the shaped laser focus, the single NVs exhibit a statistic yield of 56%±11% with excellent qualities. This processing method will contribute to the integration of color centers with emerging optical elements and high-density data storage.