Methane hydrate is a new clean energy source. For the cruise detection of methane hydrate, membrane separation off-axis integrated cavity output spectroscopy, M-ICOS, is applied to detect dissolved methane (CH4) and carbon dioxide (CO2). An M-ICOS system comprises a membrane separation unit, a cavity temperature and pressure controller, an optical cavity, a spectrometer unit, and an industrial personal computer. The M-ICOS system is tested for performance evaluation. The accuracies of the temperature and pressure controller are 0.0003733 ℃ and 0.6799 Pa, respectively. The limits of detection of CH4 and CO2 are 0.56×10 -9 and 0.62×10 -6, respectively. A field experiment in Shenhu area, South China Sea, found a strong fluctuation in the gas concentration at the depth of 500--700 m, which was probably because the sea flow took high concentration gas from the methane hydrate enrichment area. Experimental results reveal that the system exhibits a good sensitivity and stability, which make it usable to detect CH4 and CO2 in deep sea for cruise detection of the methane hydrate.