A hollow waveguide (HWG) based mid-infrared gas sensor using a 2.73 µm distributed feedback (DFB) laser was developed for simultaneously measuring the concentration changes of the three isotopologues 13CO2 12CO2, and 18OC16O in exhaled breath by direct absorption spectroscopy, and then determining the 13CO2/12CO2 isotope ratio (δ13C) and 18OC16O/12CO2 isotope ratio (δ18O). The HWG sensor showed a fast response time of 3 s. Continuous measurement of δ13C and δ18O in the standard CO2 sample with known isotopic ratios for ∼2 h was performed. Precisions of 2.20% and 1.98% for δ13C and δ18O respectively at optimal integration time of 734 s were estimated from Allan variance analysis. Accuracy of −0.49% and −1.20% for δ13C and δ18O, respectively, were obtained with comparison to the values of the reference standard. The Kalman filtering method was employed to improve the precision and accuracy of the HWG sensor while maintaining high time resolution. Precision of 5.45% and 4.88% and the accuracy of 0.21% and −1.13% for δ13C and δ18O, respectively, were obtained at the integration time of 0.54 s with the application of Kalman filtering. The concentrations of 12CO2 13CO2 and 18OC16O in breath cycles were measured and processed by Kalman filtering in real time. The measured values of δ18O and δ13C in exhaled breath were estimated to be −21.35% and −33.64%, respectively, with the integration time of 1 s. This study demonstrates the ability of the HWG sensor to obtain δ13C and δ18O values in breath samples and its potential for immediate respiratory monitoring and disease diagnosis.