The invention relates to a low carbon, clean and efficient distributed energy source system and an operation method thereof, and belongs to the field of distributed energy sources. In the prior art, the development of the distributed energy source system is faced with many challenges such as carbon dioxide emission control, nitrogen oxide emission control, system efficiency improvement, heat island effect, and no comprehensive treatment method can solve the problems. The low carbon, clean and efficient distributed energy source system comprises a natural gas device, a gas distributed energy source system, a flue gas heat recovery device, a flue gas heat utilization device, a CO2 separation device, a CO2 supply terminal, a N2 separation device, a N2 supply terminal, a NOX separation device,a NOX recovery device, an O2 separation device, an O2 supply terminal and an Ar supply terminal. The low carbon, clean and efficient distributed energy source system can effectively solve the problems of carbon dioxide emission control, nitrogen oxide emission control, system efficiency improvement, heat island effect and the like, and can reasonably and effectively utilize flue gas generated bythe gas distributed energy source system.