Snow serves as a pivotal water resource in the three provinces of Northeast China (TPNC), the investigation of spatial and temporal distribution changes of snow cover is essential for the region’s efficient water resource management. The Moderate Resolution Spectroradiometer (MODIS) snow cover product has proven effective in providing detailed spatial–temporal distribution and identification of snow cover. However, its accuracy and reliability are significantly hampered by cloud obscuration. To address this issue, we have developed a novel four-step cloud removal approach, which includes Terra and Aqua combination, 5-day temporal combination, snowline method (IMS) as well as 8-pixel and 24-pixel adjacent pixel method. Results indicate that the proposed approach successfully eliminates all cloud cover, yielding a highly accurate cloud-free snow cover product with validation accuracies of 92% and 97% when using in situ snow depth measurements and cloud masking method, respectively. We investigated the spatial and temporal variations of snow cover for the TPNC during 2003–2018 with snow coverage and snow cover days (SCD) and analyzed the correlation between snow cover and climate factors. The results showed that the annual basin-averaged snow coverage increased at a rate of 1.27% yr−1 before 2009 and decreased at a rate of 1.80% yr−1 after 2009. The Mann-Kendall tests indicated that about 72% of the total area showed an increasing trend of annual SCD during 2003–2018. Conversely, 94% of the total area exhibited a decreasing trend of annual SCD for the period of 2009–2018 due to the increasing trend of temperature and decreasing trend of precipitation. Our approach shows a promising application of generating accurate cloud-free products and its potential to examine spatial–temporal variations of snow cover under climate change for other snow-covered regions globally.