Indoor Air Quality (IAQ) along with the call for energy-saving has become a hot research topic in recent years. Low ventilation rate consumes less energy but may result in poor air quality, causing health issues for occupants in the long run. Conventional ventilation strategies often result in imbalance in multiple zones served by one HVAC system considering different number of occupants in each zone. This paper presents a model-based control of CO2 concentration for multi-zone ACB air-conditioning systems aiming at achieving a high IAQ level. A multi-zone CO2 concentration model is established which takes into account the coupling between neighbour zones. Genetic Algorithm (GA) and Least Squares Method (LSM) are used for parameter identification of the CO2 model. A control strategy is proposed for the intake airflow rate so that the desired level of the CO2 concentration can be achieved in the presence of varying number of occupants. Simulations are given to validate the proposed control design.