Carbon aerogels possess exceptional mechanical strength, compression elasticity, and fatigue resistance, making them indispensable in various industries, including energy storage devices, sensors, and spacecraft, particularly in demanding environments. Recent studies have demonstrated that the creation of ordered layered porous structures can be achieved through the design of material systems, regulation of microstructure, and improved preparation techniques. This article presents a comprehensive analysis of the manufacturing methods and factors that influence the three-dimensional (3D) ordered structure of carbon aerogels. Here, we give an extensive review of the manufacturing methods and factors that influence the 3D ordered structure of carbon aerogels. In recent years, there has been a growing emphasis on the precise 3D manufacturing of carbon aerogels and their manipulation. Various methods, such as chemical vapor deposition, freeze casting techniques (using ice templates), chemical reduction and cross-linking, and carbonization of porous structures, have been developed by researchers. Additionally, this study aims to examine the interconnections and variables that impact the mechanical properties, electrical conductivity, thermal conductivity, and other anisotropic characteristics of carbon aerogels with a 3D ordered structure. Drawing from the existing advancements in this field, we also identify potential issues associated with highly ordered carbon aerogels and outline future challenges in terms of synthetic techniques and structural manipulation. This review will provide guidance for controlling highly ordered carbon aerogels, promoting the application of ordered carbon aerogels.