Real-time blood gas analysis is of great significance in disease diagnosis and treatment. Here we have developed a pH, PO2 and PCO2 multifunctional fluorescent capillary sensing system. The pH, O2 and CO2 fluorescent indicators with same excitation wavelength are fixed into a single capillary tube. The sensing system possesses sensitive fluorescence response to pH, O2 and CO2, and the changes of pH, O2 and CO2 in buffer, in vitro, and in vivo can be detected simultaneously by measuring the fluorescence signals of sensor probe. The PO2, PCO2 and pH of rabbits in four disease models were assessed efficiently by the sensing system, exhibiting similar variation trend with the results by blood gas analyzer. Studies in living rabbit display the reasonable and favorable feasibility of capillary sensing system in real-time arterial blood gas analysis. Overall, the multifunctional fluorescent capillary sensing system exhibits significant potential in real-time arterial blood gas analysis and clinical application of disease diagnosis.