[Objective] Air anion concentration in different ecological functional zones in southern margin of Junggar Basin was monitored in summer in order to provide a reference for rating regional air quality. [Methods] The concentrations of negative air ion in different ecological function areas (water body, forest area, parking lot, populated districts)by AIC-1000 type instrument. SPSS 17.0 was used for statistical analysis. [Results] (1) The concentrations in different regional areas ranked as: Jinghe > Hami > Tianchi > Baerluke. And the difference between the concentrations of Jinghe and Tianchi and values of Hami and Baerluke was significant (p<0.05); (2) In local ecological function areas, water body and forest area had higher concentration of negative air ions; and the daily concentration showed that it was higher in the morning and evening, and lower in the noon; (3) The rank of air quality levels(CI): Tianchi (level A, 1.28±0.42 ind/cm³) > Jinghe (level A, 1.16±0.08 ind/cm³) > Hami (level D, 0.33±0.14 ind/cm³) > Baerluke (level D, 0.32±0.03 ind/cm³); (4) Weather conditions could also influence the concentration of negative air ions, a rank was measured as: rainy(699 ind/cm³) > dust(507 ind/cm³) > sunny(428 ind/cm³) > cloudy(395 ind/cm³). [Conclusion] Changes in air quality and the concentration of negative air ions were basically synchronized in different ecological function areas. Air quality along the southern Junggar Basin showed an inferior-superior-inferior trend graphically form east to west.