Isoprene is a typical physiological marker that can be used to screen for chronic liver disease (CLD). This work developed a portable micro-integrated chromatography analysis system based on micro-electromechanical system (MEMS) technology, nanomaterials technology and embedded microcontroller technology. The system integrated components such as graphene oxide quantum dots (GOQDs) modified semi-packed microcolumn, In2O3 nanoflower (NF) gas-sensitive detector and 3D printed miniature solenoid valve group. The effectiveness of the separation effect of the micro-integrated system was verified by gas mixture test; the laws of the influence of carrier gas pressure and column temperature on the chromatographic separation performance, respectively, were investigated, and the working conditions (column temperature 90 °C and carrier gas pressure 7.5 kPa) for system testing were determined. The percentages of relative standard deviation (RSD) of the peak areas and retention times obtained for the separated gases were in the range of 0.95% to 6.06%, indicating the good reproducibility of the system. Meanwhile, the microintegrated system could detect isoprene down to 50 ppb at small injection volume (1 mL). The system response increased with increasing isoprene concentration and was linearly correlated with isoprene concentration (R2 = 0.986), indicating that the system was expected to be used for trace detection of isoprene, a marker gas for liver disease, in the future.