Abstract: Surface proteins play pivotal roles in physiological processes, including cell recognition, signal transduction, substance transport, and immune responses. However, challenges persist in characterizing abnormal surface proteins in disease states and identifying therapeutic targets, due to the low abundance of these proteins within the total proteome and the frequent presence of their complex glycosylation modifications. Recent years have witnessed the vigorous development of chemical proteomics, leading to the successful creation of various chemical probes for the labeling and characterization of cell surface proteins. These techniques have subsequently been applied to the detection of disease surface proteins and the discovery of corresponding targets. Surface protein characterization techniques based on chemical proteomics are discussed herein, focusing on the principles of amino acid-targeted labeling, proximity labeling, and glycoprotein capture. The novelty, advantages, and limitations of techniques such as targeted lysine labeling, peroxidase and photocatalytic proximity labeling, and chemical glycan capture and metabolic glycan labeling are elaborated, and their applications across various biological models and disease types are described, aiming to provide some reference for target discovery and drug development targeting surface proteins.