The atmospheric vertical structure and changed characteristics of boundary layer parameters, as well as their relations with sea ice and temperature changes in the center of Arctic Ocean(80°–88°N) are presented by adopting GPS sounding data obtained by the 4th–6th Arctic expeditions of China and NCEP(National Centre for Environmental Prediction) reanalysis data. Obvious differences are observed regarding the tropopause, boundary layer height, temperature inversion, and vertical structure of wind speed and direction in the center Arctic Ocean in the summer of 2012, 2010, and 2014. These differences can be explained by the relations between temperature and changes in sea ice extent in September from 1979 to 2014. In September 2012, the Arctic sea ice extent decreased by 44% an with obvious warming process. In September 2010 and 2014, it decreased by 22.6% and 17% with an obvious cooling process, respectively. A comparison of the two processes shows that sea ice change has a significant influence on the structure of the atmospheric boundary layer. In the recent 30 years, the temperature changes of 1000 and 850 h Pa in the center of the Arctic Ocean have displayed an obvious warming trend and negative correlation with sea ice extent. These changes indicate that the continuous reduction of Arctic sea ice will continue the warming of the troposphere middle layer. The atmospheric vertical structure and changed characteristics of boundary layer parameters, as well as their relations with sea ice and temperature changes in the center of Arctic Ocean (80 ° -88 ° N) are presented by adopting GPS sounding data obtained by the 4th-6th Arctic expeditions of China and NCEP (National Center for Environmental Prediction) reanalysis data. Obvious differences are observed regarding the tropopause, boundary layer height, temperature inversion, and vertical structure of wind speed and direction in the center Arctic Ocean in the summer of 2012, 2010, and 2014. These differences can be explained by the relations between temperature and changes in sea ice extent in September from 1979 to 2014. In September 2012, the Arctic sea ice extent decreased by 44% an with obvious warming process. In September 2010 and 2014, it decreased by 22.6% and 17% with an obvious cooling process, respectively. A comparison of the two processes shows that sea ice change has a signifi cient influence on the structure of the atmospheric boundary layer. In the recent 30 years, the temperature changes of 1000 and 850 h Pa in the center of the Arctic Ocean have displayed an obvious warming trend and negative correlation with sea ice extent. that the continuous reduction of Arctic sea ice will continue the warming of the troposphere middle layer.