The coupling between a thermal and an airflow model is required for accurate simulation of natural or mechanical (hybrid) ventilation systems. Generally, two coupling approaches exist: "ping-pong" and "onion". Prediction of temperature and airflow rate between zones can be significantly influenced depending on the coupling method and selected time step. Therefore, this paper aims to find the appropriate coupling method and time step for three different systems (hybrid ventilation, energy recovery ventilator, and natural ventilation) in an apartment. For this purpose, EnergyPlus (thermal model) and CONTAMW (airflow model) were coupled in the MATLAB platform. It has been concluded that simulation outputs are dependent on the coupling methods and chosen time step. HVAC engineers and simulationists are required to carefully choose a coupling method as well as time step based on the systems of their interests.