The promotion on energy conservation and efficiency improvement relies on the comprehensive understanding of the urban energy metabolic mechanism, especially of the impacts related to heterogeneity within the urban energy metabolic processes. In this paper, the gravity model is introduced to analyze the attribute differences of the connecting nodes on each side of the energy flows within urban energy metabolic processes. Using Beijing’s main departments associated with the non-capital functional dispersal policies as the case study, three fossil energy including coal, oil and natural gas are included in the empirical analysis to evaluate the induced impacts within Beijing’s energy metabolism due to the heterogeneity of departments. Based on the scenario analysis that consists of six combinations of two intensities of energy optimization and three intensities of department dissolution, results suggest that both the positive and negative feedback mechanisms of different factors on the departments’ energy consumption and the degree of preference for different energy in different departments are heterogeneous. The heterogeneity causes different policy scenarios to have different effects on the optimization of the energy structure of Beijing''s non-capital functional demobilization sector. Strong optimization and strong dissolution scenarios are most beneficial to the substitution of coal and natural gas in the manufacturing department, while low dissolution but strong optimization scenarios are most beneficial to control energy consumption in the transportation industry, wholesale and retail departments. The latter also has some advantages on improving the energy consumption structure of the education industry.