Recently, two-dimensional (2D) layered materials, such as graphene and transition metal dichalcogenides (TMDCs), have garnered a lot of attention in energy storage/conversion-related fields due to their novel physical and chemical properties. Constructing flat graphene and TMDCs nanosheets into 3D architectures can significantly increase their exposed surface area and prevent the restacking of adjacent 2D layers, thus dramatically promoting their applications in various energy-related fields. Chemical Vapor Deposition (CVD) is a low-cost, facile, and scalable method, which has been widely employed to produce high-quality graphene and TMDCs nanosheets with 3D architectures. During the CVD process, the morphologies and properties of the 3D architectures of such 2D materials can be designed by selecting substrates with different compositions, stacking geometries, and micro-structures. In this review, we focus on the recent advances in the CVD synthesis of graphene, TMDCs, and their hybrids with 3D architectures on different 3D-structured substrates, as well as their applications in the electrocatalytic hydrogen evolution reaction (HER) and various secondary batteries. In addition, the challenges and future prospects for the CVD synthesis and energy-related applications of these unique layered materials will also be discussed.