In the present study, the basic energy flows, forming the microclimate of buildings with green roofs were been presented. Based on the finite differences method, a mathematical model has been developed, describing the building energy exchange processes. For this purpose each element of the building (walls, floor, roof) has been divided into multiple bordering layers and the temperature curve of each one of them was estimated using the heat fluxes entering from the bordering layers. The indoor air temperature was then estimated using the building element’s internal surface. The model’s algorithm is presented in a block-scheme, describing the sequence of evaluations. The developed model allows the microclimate inside buildings with green roofs to be modeled and simulated for different climate zones and insulation parameters.