DNA origami-assisted nanolithography (DOANL) for fabricating custom-designed nanomaterials through pattern transfer from DNA origami to different substrates materials are presented. However, the pattern's integrity and resolution face considerable challenges due to the uncontrollable growth of the nanomaterials during transformation and the unclear mechanism of DOANL. Herein, we report a DOANL combined with area-selective atomic layer deposition (ALD) strategy for fabricating custom shapes hafnium oxide (HfO₂) with the high-fidelity and high-throughput. We find that the HfO₂ selectively grows on DNA origami substrates in a hydroxyl-rich area instead of a methyl-rich protective layer. Combined with the merit of the area-selective ALD method, the HfO₂ atom selectively coated on the DNA origami surface, thus, precisely modeling the shapes with high-precision in our study based on the surface groups difference of DNA origami and the naked hexamethyldisilane (HMDS)-treated substrates, which reveal the mechanical of high-fidelity pattern transfer based on DOANL. As a result, DNA origami structures can program the shape of HfO₂ nanostructures. The DOANL that is based on the principle of "bottom-up" precision assembly breaks through the shape complexity and high-throughput fabrication limitation of the HfO₂ nanostructures, including two- and three-dimensional structures, plane and curved structures, monolithic and hollow structures. Based on the "top-down" accurate fabrication principle, the area-selective ALD on methyl-rich protective layer substrates improves the integrity and resolution of the pattern transfer process. Overall, this work provides a general technology for nanofabrication strategy.