Studies on spatial-temporal differentiation of regional carbon imbalance based on urban functional zoning will be beneficial in understanding the mechanism of urban function pattern affecting urban compound ecosystem carbon cycle. Xiamen city, with its 6 administrative districts, was taken as a study case and statistical data and land-use data processed by satellite image were adopted. Carbon emissions and carbon sinks were accounted for each district in different historical periods by using simplified accounting models. The results showed aggravating imbalance trend in overall carbon budget of Xiamen city, in 2013 C0_2 emissions were 7.44 times more than C0_2 sequestration, compared to 1.91 times in 2003, and carbon imbalance condition distribution has spatial-temporal heterogeneity. Combined with the main regional functions of city development planning, we discuss the mechanism and process of social economic indicators and landscape, which are most influenced by the main functions, affecting the temporal and spatial change of regional carbon imbalance. We conclude that specific carbon abatement or carbon offsetting policies should be considered to address the regional main functions based on individual current carbon imbalance condition. This highlights the importance of urban planning in maintaining regional carbon balance. The aggravating climate change caused by urbanization will require reasonable urban functional zoning with the consideration of urban ecological services.