Some human exhaled volatile organic compounds (VOCs) can be employed to diagnose related human endogenous diseases as characteristic biomarkers, which is expected to be applied to rapid screening and grading because of their non-invasive and cost-effective advantages. In this study, we developed a compact gas chromatography (GC) platform mainly composed of an integrated silicon-based micro-column chip using micro-electromechanical system techniques and a miniaturized metal oxide semiconductor gas detector. In addition, the sampling/switching valve with related components and embedded microcontrollers was used for airflow control. The fabricated system selectively detected the five VOCs (pentane, acetone, toluene, octane, and decane) considered the typical endogenous disease biomarkers. In the experiments, the functional parameters of the system were investigated, and the optimum temperature conditions of the system for separation were determined. The results show that the system can successfully test the studied five VOCs as low as 1 ppm. In addition, the influence of interfering gas (carbon dioxide and ammonia) on the system for the VOC mixture is also investigated. Moreover, to prove the possibility of breath analysis of the fabricated system, the detection performance of isoprene and acetone at the ppb level is studied. Then, the concentration changes of the isoprene at the ppb concentration for human breath are successfully detected in the system. Therefore, we believe that the prepared compact GC system has potential applications in the human endogenous disease diagnosis for the VOC biomarkers.