The poor indoor air quality (IAQ) of severely polluted toilets is associated with increased risk of severe disease. This study aimed to evaluate the overall IAQ according to the contaminant removal efficiency, volume average concentration, and breathing zone control level. The characteristics of contaminant transmission in a non-flushing ecological toilet (NFET) were analyzed using the computational fluid dynamics (CFD) methodology, and the proposed model was further validated based on experimental measurements. Both an orthogonal experimental design and CFD were used to analyze factors such as exhaust fan position (EFP), air change rate per hour (ACH), natural vent location (NVL), and grid height (G-h). The EFP and ACH were demonstrated to be the dominant factors affecting the IAQ, whereas NVL and G-h were found to play key roles. Single-factor analysis based on the significance levels of the ACH, EFP, and NVL was conducted using the CFD methodology to define three exhaust behaviors—namely, “ineffective”, “enhanced”, and “excessive”. These results provide key insights that may be used to improve the IAQ of NFETs.