Due to their high biological activity, low toxicity, and superior biocompatibility, peptides are often utilized in cancer therapy, cellular activity simulation, and antibody detection. As a result, the detection and analysis of peptides has grown into a significant area of research. The direct detection of peptides by mass spectrometry frequently encounters significant interference, and the outcomes are frequently disappointing. Organic frameworks with plentiful pore size, large specific surface area, and simple surface functionalization are currently prevalent materials for peptide enrichment. Metal-organic frameworks (MOFs) and covalent-organic frameworks (COFs) have been used for enriching glycopeptides, phosphopeptides, and endogenous peptides.Protein glycosylation and phosphorylation are the most common post-translational modifications of proteins. Since common organic frameworks have a limited affinity for post-translationally modification peptides and their enrichment impact is not what is expected, several researchers have tried to design functional organic framework materials to obtain effective peptide enrichment. Hydrophilic nanoparticles have a particular affinity for glycosyl groups and have the distinct benefit of not creating enrichment bias when capturing glycopeptides. Hydrophilic organic framework materials may be changed with hydrophilic groups, hydrophilic chemicals, and magnetic functionalization to enhance glycopeptides through hydrogen bonding, electrostatic interactions, and van der Waals forces, building on the synthesis of hydrophilic nanomaterials. The great majority of organic frameworks are made up of organic ligands that particularly bind to phosphate group.The chelation between metals, metal oxides, and phosphate groups provides the basis for capturing the peptides by organic frameworks. Therefore, in order to achieve effective phosphopeptide enrichment, numerous organic frameworks have tried to increase the affinity between organic frameworks and phosphate groups by ligand replacement, ionic ligand modification, and modification. This paper focuses on the principles and applications of MOFs and COFs for peptide enrichment in the last five years.