A general methodology is presented to include a multi-layer approach for the in and above canopy air while keeping single-layer model simplicity of coupling and efficiency. This is a major change in the type of model (from single-layer to multi-layer). The formulation to include air prognostic layers in the surface scheme is derived from the atmospheric equations. New variables are wind, temperature, humidity and Turbulent Kinetic Energy (Tke). In this paper, the general methodology is presented and the evaluation for TEB against the BUBBLE dataset is presented in a companion paper (Hamdi et al.). Several advances of the TEB urban surface scheme have also been implemented in order to make the model able to answer new issues arising in our field. Vegetated areas are included in the street which is necessary to evaluate climatic performance of urban trees, lawns, gardens at the scale of the city. A modification offers the possibility to give preferred orientations to the streets so that the model is better simulate pedestrian level comfort. Finally, the last modifications are the inclusion of windows and a finer energy balance for the building interior.