Models-3 is a system framework that helps users build, apply, and study regulatory or customized environmental models. The Community Multi-scale Air Quality (CMAQ) Model is the initial operating science model under the Models-3 framework. It integrates developments in physical and chemical science process algorihtms together with efficient numerical algorithms and data intercommunication methods. The CMAQ system consists of emissions processing, meteorological modeling, and chemistry-transport modeling. A significant effort has been made to maintain consistent scientific formulations throughout the modeling process. In this paper, the authors describe the high-level architecture, the modular design concept, and the key implementation features of CMAQ.