On the basis of defining the connotation and structural elements of atmospheric environmental self-cleaning capability, this paper systematically analyses the synergy mechanism of atmospheric environment self-cleaning capability, and puts forward the system optimization of atmospheric environmental self-cleaning capability. The self-cleaning ability of the atmospheric environment mainly includes nature’s ability to cleanse itself and rationality of human design. The synergy mechanism of self-cleaning capability of nature mostly refers to the fact that pollutants in the atmosphere can be transformed chemically or scavenged by means of the dry deposition, wet deposition, transportation and dispersion of atmospheric hydrometeors, such as rain, snow, wind, geography, humidity and the like. The synergy mechanism of rationality of human design chiefly refers to the human ability to take a variety of comprehensive prevention and control measures such as reasonable urban planning, wind tunnel design, hydraulic facilities, pollution source layout and others to make the most of nature’s self-cleaning capability and the ability to reduce the impact of the atmospheric pollutants. On this basis, seven measures have been proposed system optimization of atmospheric environmental self-cleaning capability. First, we should quicken the construction of artificial wetlands in areas with lower atmospheric self-cleaning capability; second, we should rapidly improve the vegetation coverage rate in the areas with low atmospheric self-cleaning capability; third, we should systematically plan urban construction in areas with lower atmospheric self-cleaning capability; fourth, we should scientifically construct urban air ducts in the area with low atmospheric environment self-cleaning capability; fifth, we should work out scientific production plans for the pollution intensive industries and gradiently transferring pollution intensive industries; sixth, we should vigorously propel the ecological migration work in areas with lower atmospheric self-cleaning capability; seventh, we should strengthen the construction of a linkage system of atmospheric environment self-cleaning capability.