Abstract: The composition and content of volatile organic compounds (VOCs) in exhaled breath are closely related to change in the human physiological state. Some biosignature molecules generated by human metabolism, including disease marker molecules, are expelled from the body via exhaled breath. By accurately detecting disease markers in exhaled breath, the onset and progression of relevant diseases can be effectively monitored. The rapid development of modern breath analysis techniques, including electronic nose (E-nose) sensor systems, gas chromatography-mass spectrometry (GC-MS), selected ion flow tube mass spectrometry (SIFT-MS), proton transfer reaction mass spectrometry (PTR-MS), and extractive electrospray ionization mass spectrometry (EESI-MS), has provided rapid, non-invasive detection methods for disease diagnosis and progression monitoring. Among these techniques, E-nose sensor systems are characterized by portability and rapid screening capabilities. GC-MS serves as the gold standard for offline analysis due to its strong qualitative and quantitative capabilities. Real-time online techniques, including SIFT-MS and PTR-MS, are noted for their speed and sensitivity. EESI-MS enables direct analysis of complex samples. In recent years, research on exhaled biomarkers for disease diagnosis and treatment has been conducted on a wide range of diseases. For example, acetone in human exhaled breath can serve as a potential marker for diagnosing diabetes; hydrogen produced in breath after lactose intake is a potential marker for diagnosing gastrointestinal disorders; isotope-labeled carbon dioxide (¹³CO₂) produced in breath after ingesting ¹³C-labeled urea serves as a marker for detecting Helicobacter pylori infection. However, there are significant differences in the types, content, diagnostic sensitivity, and specificity of disease markers obtained by different researchers using various methods. Factors such as poor comparability and lack of standardization severely constrain scientific research and the development of related industries. Therefore, standardization requirements are critical in three key areas. Firstly, breath sampling protocols vary significantly. Factors such as collection methods, subject’s physiological states, and environmental VOC contamination profoundly impact results and comparability. Secondly, analytical instruments, especially sophisticated mass spectrometers, require reference standards and calibration protocols to ensure consistent performance and inter-laboratory comparability, including addressing instrument background and sensitivity drift. Thirdly, the complexity and instability of breath matrices make the development of reliable reference materials for calibration and quality control extremely challenging, thereby hindering accurate quantification and method validation. This paper summarized detection techniques for VOCs in exhaled breath, discussed advances in breath biomarker research, and analyzed current challenges in standardized sampling procedures, analytical instruments, and reference materials. The perspectives provided herein are intended to serve as a reference for future research on breath-based disease diagnosis.