Microgrids have a strong ability to generate local power and consume renewable energy, which can solve the problems of power supply shortages and greenhouse gas emissions created in the process of social development. The honeycombed active distribution network (HADN) can flexibly, independently, and interconnectedly operate microgrids through power exchange stations, so appropriate HADN dispatch can produce increased low-carbon benefits than general microgrids. In this study, we first designed a model for optimizing HADN with the lowest carbon emission as the target, then we introduced the concept of carbon emission flow into the optimization process to determine the carbon emission level of each element. Finally, we illustrated and verified the proposed model by a HADN composed of three microgrids. The optimization results of the case study showed that by scheduling the DGs within the microgrids, the total carbon emissions of the system were reduced from 123,328.1 to 117,688 kg CO2; the system with a HADN structure was able to produce only 110,958 kg CO2 and effectively reduce carbon emissions by 10%, which proved that HADN can be scheduled with high flexibility and provides increased low-carbon performance through the proposed optimization dispatch method.