Our study shows that, during 2001–2017, when the sea ice was melting rapidly, cyclone days accounted for more than 50% of the total autumn days at the sounding stations in the Arctic marginal seas north of the Eurasian continent and almost 50% of the total autumn days at the sounding station on the northern coast of Canada. It is necessary to investigate the influence of Arctic cyclones on the cloud fraction in autumn when the sea ice refreezes from its summer minimum and the infrared cloud radiative effect becomes increasingly important. Cyclones at the selected stations are characterized by a narrow maximum rising zone with vertically consistent high relative humidity (RH) and a broad region outside the high RH zone with low RH air from the middle troposphere covering the low troposphere’s high relative humidity air. Consequently, on approximately 40% of the cyclone days, the cloud formation condition was improved from the near surface to the upper troposphere due to the cooling of strong rising warm humid air. Therefore, cyclones lead to middle cloud increases and sometimes high cloud increases, since the climatological Arctic autumn clouds are mainly low clouds. On approximately 60% of the cyclone days, only low cloud formed, but the low cloud formation condition was suppressed due to the mixing ratio decrease induced by cold dry air sinking. As a result, cyclones generally lead to a decrease in low clouds. However, the correlation between the cyclones and low clouds is complex and varies with surface ice conditions.