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Nanostructured materials (NMs) are the materials with a microscopic structure of 1–100 nanometers. NMs can outperform their bulk counterparts, due to their reduced sizes. In terms of dimensionality, NMs can be classified into zero-dimension (0D), 1D, 2D, and 3D. Atomic and molecular layer deposition (i.e., ALD and MLD) are two unique techniques for fabricating and designing novel NMs, featuring their unique capabilities for material growth with excellent uniformity, unrivaled conformal coverage, and precise controllability at low temperature. As a result, a large variety of NMs by ALD and MLD have found applications in a wide range of areas. In this work, we focus on summarizing the strategies of ALD and MLD for various NMs and exemplify their applications in surface engineering and new energies.