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Many global climate models (GCMs) have difficulty in simulating climate variabilities over high northern latitudes. One of the main reasons is the inability of GCMs to simulate proper cloud fraction and the amount of liquid-containing cloud over the region. This study assessed the impact of cloud simulation in high latitudes by comparing the long-term parallel simulations of Community Atmosphere Model version 6 (CAM6) and CAM5, the previous version. The results show that the CAM6 simulation exhibits a considerable improvement in the Arctic, especially by reducing the cold bias of CAM5 throughout the year. Over the sub-Arctic region, however, CAM6 produces an excessive cold bias in summer and a warm bias in winter compared to the observation, which is closely related to the overestimation of cloud fraction and the amount of cloud liquid. In summer, the overestimation of the cloud in CAM6 tends to alleviate the cold bias compared to CAM5 due to an increase in downward longwave radiation over the high latitudes, while causing the excessive cold bias by blocking downward shortwave radiation over the sub-Arctic land area. In winter, when there is little incidence of shortwave radiation, the overestimation of the cloud in CAM6 increases the downward longwave radiation, which alleviates the cold bias in CAM5 over the Arctic but induces an excessive warm bias over the sub-Arctic land. The excessive cloudiness in CAM6 could weaken the high-latitude internal variability, exacerbating the deteriorating climate variability and long-term trend simulations in the region.