Carbon dioxide (CO2) and humidity are two factors that affect respirator comfort. Whenever one uses a respirator, CO2 is reinhaled from the previous exhalation and the humidity inside the respirator cavity increases. The CO2 reinhalation causes respirator discomfort with symptoms like headache, dizziness, and etc. The increased humidity causes respirator thermal discomfort. Experimental researches focused on measuring the CO2 and humidity values in the respirator cavity during a long period of time (over 1 hour). However, these experiments ignored CO2 and humidity value variation during a breathing cycle within the respirator cavity. The objective of this study was to use computational fluid dynamics (CFD) method to calculate the CO2 and humidity values inside the respirator cavity during four breathing cycles (19.2s). In our previous work the contact between a headform and a filtering facepiece respirator (FFR) was simulated by the using finite element modeling. In this work a meshed domain was generated including the FFR cavity, the FFR and the region outside of the FFR. A breathing cycle, having both exhalation and inhalation, was then defined as a time-dependent flow rate through a breathing opening (nasal breathing, mouth breathing, and nasal-mouth breathing). Using CFD method, the breathing air flow and the species transport of CO2 and water vapor (H2O) in the domain were simulated for 4 breathing cycles. Totally 5 tests with different breathing openings and different breathing flow rates were conducted: nasal breathing with base, 2 and 3 times flow rate, mouth breathing with base flow rate, and nasal-mouth breathing with base flow rate. The simulation results showed that there were large CO2 and H2O value variations (CO2 mass fraction from 0 to 0.074 and H2O mass fraction 0.0077 and 0.0151) in the FFR cavity during a breathing cycle. The inhaled CO2 mole fraction decreased with increasing breathing flow rate. With the base flow rate, during inhalation the middle point between the nostrils and mouth had higher relative humidity than other probing positions did.