Settlement morphology transition is triggered by rapid urbanization and urban expansion, but its relationships with residents commuting energy consumption remains ambiguous. It is of significance to understand the controlling mechanisms of sustainable public management policies on the energy consumption and greenhouse gases emission during the process of urban settlement morphology transition. Taking the Xiamen City of East China as a case, and by using the integrated land use and transportation modeling system TRANUS, a scenario analysis was made to study the effects of urban settlement morphology transition on the urban spatial distribution of population, jobs, and land use, and on the residents commuting energy consumption and greenhouse gasses emission under different scenarios. The results showed that under the Business As Usual (BAU) scenario, the energy consumption of the residents at the morning peak travel time was 54.35 tce, and the CO2 emission was 119.12 t. As compared with those under BAU scenario, both the energy consumption and the CO2 emission under the Transition of Settlement Morphology (TSM) scenario increased by 12%, and, with the implementation of the appropriate policies such as land use, transportation, and economy, the energy consumption and CO2 emission under the Transition of Settlement Morphology with Policies (TSMP) scenario reduced by 7%, indicating that urban public management policies could effectively control the growth of residents commuting energy consumption and greenhouse gases emission during the period of urban settlement morphology transition.