Observation of concentration of pollutants in atmosphere by OPSIS AB DOAS system and Thermo SCIENTIFIC EMS system was performed in rural areas of Nanjing during the winter of 2009 and the spring of 2010.Based on technical characteristics of the two systems,quality control of the observation data and comparison of the two systems were carried.The characteristics of seasonal variations of mass concentration of NO2,O3 and SO2 were analyzed.The comparison of pollution characteristics between urban and rural areas measured by the two different systems during the autumn of 2009 was also carried.Quite good correlation can be established between the observation data of the two systems.The observation data of DOAS system are influenced by water vapor and aerosols in atmosphere,so they are generally higher than that of EMS system,with a rate from 14％ to 25％.The concentration of SO2 and NO2 are higher in winter,while that of O3 is lower,however,quite the reverse is true in spring.There is negative correlation between the curve of NO2 and O3.The concentration of NO2 in urban areas is higher than that in rural areas,and the diurnal variation shows two peaks,while that shows one peak in rural areas.The diurnal variation of O3 shows one peak in both urban and rural areas,but the former has a bigger variation range.The diurnal variation of SO2 shows one peak in urban areas and two peaks in rural areas.