The coupled heat, air and moisture transfer between building envelopes and indoor air is complicated, and has a significant influence on the indoor environment and the energy performance of buildings. In the paper, a model for predicting coupled multi-zone hygrothermal-airflow transfer is presented. Both heat and moisture transfer in the building envelope and multi-zone indoor airflow are simultaneously considered; their interactions are modeled. The coupled system model is implemented into Matlab–Simulink, and is validated by using a series of testing tools and experiments. The new program is applied to investigate the moisture transfer effect on indoor air humidity and building energy consumption in different climates (hot-humid, temperate and hot-dry climates). The results show that not accounting for hygrothermal effects in modeling will result in overestimation of energy costs for hot and humid climate situations and possible over sizing of plant leading to inefficient operation.