Reliable cloud masks in Moderate Resolution Imaging Spectroradiometer (MODIS) snow cover products have a high potential to improve the retrieval of snow properties. However, cloud–snow confusion is a popular problem in MODIS snow cover products, especially in boreal forest areas. A large amount of forest snow is misclassified as clouds because of the low normalized difference snow index (NDSI), and excessive cloud masks limit the application of snow products. In addition, ice clouds are easily misclassified as snow due to their similar spectral characteristics, which leads to snow commission errors. In this paper, we quantitatively evaluated the cloud–snow confusion in Northeast China and found that snow-covered forests and transition zones from snow-covered to snow-free areas are prone to being misclassified as clouds, while clouds are less likely to be misclassified as snow. A temporal-sequence cloud–snow-distinguishing algorithm based on the high-frequency observation characteristics of the Himawarri-8 geostationary meteorological satellite is proposed. In the temporal-sequence images acquired from that satellite, the NDSI variance in cloud pixels should be greater than that of snow because clouds vary over time, while snow is relatively stable. In the MODIS snow cover products, the cloud pixels with NDSI variance lower than a threshold are identified as cloud-free areas and attributed their raw NDSI value, while the snow pixels with NDSI variance greater than the threshold are marked as clouds. We applied this method to MOD10A1 C6 in Northeast China. The results showed that the excessive cloud masks were greatly eliminated, and the new cloud mask was in good agreement with the real cloud distribution. At the same time, some possible ice clouds which had been misclassified as snow for their spectral characteristics similar to those of snow were identified correctly.