This study demonstrates a newly proposed methodology that handles building energy modeling at urban scale using a reduced-order energy calculation engine with geographical information system (GIS). GIS provides general building information that either directly serves as model parameters, or links to the specific prototype building models for more detailed building and system specifications. Actual urban environment was considered by quantifying the micro environment boundary conditions in terms of mutual shading and urban heat island (UHI) effect through urban morphology. A case study of Manhattan, New York was presented to demonstrate the process. The calculation result and future extensions were discussed.