Given continuous developments in industrial and scientific research, the separation and analysis of complex systems with high sensitivity, throughput, and selectivity is facing new challenges. Chromatography plays an irreplaceable role in separation science and is widely applied in environmental monitoring, pharmaceutical analysis, and food safety. Owing to their outstanding advantages, such as high loading capacity, precise quantification, and good reproducibility, chromatographic separation techniques based on various retention mechanisms have been utilized to detect different analytes. The stationary phase is the core material of chromatographic columns and has an extremely important influence on their separation performance. The selectivity and efficiency of separation largely depend on the chromatographic stationary phase. However, traditional stationary phases, such as silicon-based matrices, are characterized by complex preparation processes, poor permeability, large mass transfer resistance, and a narrow pH range. In addition, polymer matrices show poor mechanical stability and susceptibility to swelling, which limit their applications in the field of separation. Therefore, the development of novel stationary phases with the advantages of traditional stationary phases has become a research emphasis in the field of analytical science in efforts to meet separation requirements under different environments. Various stationary phases based on novel porous materials, such as metal organic frameworks (MOFs), porous organic cages (POCs), and covalent organic frameworks (COFs), are used for chromatographic separation. As mesh crystalline porous materials, MOFs have the advantages of a large surface area, adjustable structure, and easy functionalization; thus, they are widely used as chromatographic stationary phases in reverse-phase chromatography, hydrophilic-mode chromatography, mixed-mode chromatography, and other separation modes. However, because the pore size of MOFs is small and most MOFs demonstrate poor chemical stability under acidic or alkaline conditions, their applications in chromatographic separation are greatly limited. COFs are porous, crystalline polymer materials composed of light elements (H, O, C, N, B, and Si) connected via covalent bonds. Their advantages include a low density, large specific surface area, high porosity, good chemical and thermal stability, regular pores, and adjustable pore sizes. Because of their unique structures and properties, COFs are widely used in many fields such as catalysis, enrichment, gas capture, and sensing. COF materials are also suitable for separation analysis and considered ideal materials for novel chromatographic stationary phases. This review summarizes the latest research progress on the preparation and applications of COF-based chromatographic stationary phases over the past five years. First, the preparation of COF-based stationary phases (SiO2@COFs stationary phase, COFs monolithic stationary phase, pure COFs stationary phase and COFs-coated stationary phase) is introduced. The latest applications of COF-based stationary phases in the separation of organic compounds, isomers, and chiral compounds are then described in detail. Finally, the future development trends and challenges of chromatographic stationary phases based on COFs are discussed to provide new ideas for the future design and development of novel chromatographic stationary phases based on COFs.