The spatial structure and multi-scale feature of the atmospheric pollution influence domain of Beijing and its peripheral area (a rapidly developed city agglomeration) is dissected and analyzed in this paper on the basis of the atmospheric pollution dynamic-chemical process observation data of the urban building ensemble boundary layer of the Beijing City Air Pollution Observation Experiment (BECAPEX) in winter (February) and summer (August) 2003, and relevant meteorological elements and satellite retrieval aerosol optical depth (AOD) etc comprehensive data with the dynamic-statistical integrated analysis of “point-surface” spatial structure. Results show that there existed significant difference in the contribution of winter/summer different pollution emission sources to the component character of atmospheric pollution, and the principal component analysis (PCA) results of statistical model also indicate that SO2 and NOX dominated in the component structure of winter aerosol particle; instead, CO and NOX dominated in summer. Surface layer atmospheric dynamic and thermal structures and various pollutant species at the upper boundary of building ensembles at urban different observational sites of Beijing in winter and summer showed an “in-phase” variation and its spatial scale feature of “influence domain”. The power spectrum analysis (PSA) shows that the period spectrum of winter/summer particle concentration accorded with those of atmospheric wind field: the longer period was dominative in winter, but the shorter period in summer, revealing the impact of the seasonal scale feature of winter/summer atmospheric general circulation on the period of atmospheric pollution variations. It is found that from analyzing urban area thermal heterogeneity that the multi-scale effect of Beijing region urban heat island (UHI) was associated with the heterogeneous expansion of tall buildings area. In urban atmospheric dynamical and thermal characteristic spatial structures, the turbulent scale feature of the urban boundary layer (UBL) of architectural complexes had important impact on the multi-scale feature of urban atmospheric pollution. The comprehensive analyses of the variational analysis field of Moderate Resolution Imaging Spectroradiometer (MODIS) AOD-surface PM10 under the condition of clear sky and the correlation resultant wind vector field for pollution source-tracing suggest that the emission sources for winter Beijing atmospheric pollution aerosols particle might be remotely traced to the south peripheral greater-scale spatial range of Hebei, Shandong, and Tianjin etc, and the spatial distribution of the high value area of AOD was associated with that of the high value area of resident family number (heating surface source). The backward trajectory feature of winter/summer air particles exhibits analogous multi-scale feature, and depicts the difference in the scale feature of the pollution sources spatial distribution in different season. The peripheral source trajectory paths of urban atmospheric pollution (UAP) mainly come from the fixed industrial surface source or heating surface source in the outskirt of Beijing, and the diffusion and transport distance of peripheral sources in winter is larger than one in summer. The above conclusions depict the multi-scale spatial influence domain and seasonal features caused by UAP source influence and atmospheric dynamical structure. The high value area of the winter Total Ozone Mapping Spectrometer (TOMS) AOD lay in the Beijing region and its south peripheral area, an S-N zonal pattern, which reflects the dynamical effect of peripheral topographic pattern on the diffusion of regional scale atmospheric pollution sources. Study suggests that the extent of winter atmospheric pollution within the “valley” megarelief in Beijing and periphery was close related with the pollution emission sources of the south peripheral area; and the significant “anti-phase” variation feature of winter AOD and sunshine duration in Beijing and its peripheral areas, and the regional scale correlation of low cloud cover, fog days, and aerosols reflects the local climatic effect of aerosol influence in this region. Besides, analysis of the impacts of atmospheric dry/wet deposition distributions within a valley-scale on the regional water body of Miyun Reservoir also reveals the possible influence of the multi-scale spatial structure of summer water, soil and atmospheric pollution sources on the water quality of Miyun Reservoir.