The understanding of the cockpit environment with regard to air quality and contaminant suspension is currently very limited. With the escalating concerns of pilots’ health and flight performance being revealed with association to these two aspects, this study numerically investigated the air quality and CO₂ lock-up phenomenon in pilots’ local environment based on the actual dimensions of widely used aircraft prototype—Boeing 737, using computational fluid dynamics (CFD) approach. Three ventilation layouts and configurations with real operational conditions were considered and their performance and effectiveness in diluting the contaminants (CO₂) released from pilots’ mouths, were carefully assessed with the indoor air-related indices. The results revealed that only relying on the cockpit diffusers could hardly achieve a good air mixing from the pilots’ breathing level while activating the windshield inlets and personal gaspers could both be effective. Using the personal gaspers was found the most cost-effective way to facilitate the local air mixing in the breathing zone. The current three ventilation strategies were not optimal in minimising the CO₂ concentration in pilots’ micro-environment. Significant CO₂ lock-up phenomenon with concentrations from 700 to 1000 ppm can be noticed. When the design priority is to effectively minimise the local contaminant in pilots’ breathing zone, appropriately changing the location of the vents could be more effective than increasing the mass flow rate. With current ventilations, nearly 6%–15% of pilots would fail the pilot manoeuvring performance under the FAA Practical Test Standards and from a healthy perspective, several sick building syndromes can be initiated, such as nose/sinus irritation, sore throat, and wheeze.