Hyphenated techniques in the field of analytical chemistry involve combining different analytical methods to enhance the analysis of samples. One common approach is to combine chromatographic techniques with spectroscopic techniques. This makes it possible to comprehend the component included in a mixture on a more thorough level. It contains the various techniques such as GC-MS, LC-MS, LC-NMR, CE-MS, and LC-IR etc. Overall hyphenated technique offer improved analysis of samples in terms of specificity, accuracy, and precisions by combining multiple analytical methods, scientists can obtain more comprehensive information about the components. Capillary electrophoresis-mass spectrometry (CE-MS) has emerged as a powerful analytical tool for the comprehensive analysis of complex biological samples. This review provides a comprehensive overview of the latest advances in sophisticated hyphenated analytical techniques within the realm of CE-MS. It highlights the synergistic combination of capillary electrophoresis with mass spectrometry, showcasing its applications in proteomics, metabolomics, pharmaceutical analysis, and clinical diagnostics.