As an important part of the cryosphere, lake ice is a sensitive indicator of climate change. Remote sensing technology can quickly and accurately monitor the process of its formation and decay, among which Moderate Resolution Imaging Spectroradiometer (MODIS) images are the most widely used data in the remote sensing monitoring of lake ice. The reasonable selection of monitoring methods is of great significance to grasp the dynamic process and response to climate change of lake ice. In this study, five commonly used remote sensing monitoring methods of lake ice based on MODIS MOD09GA data, including the single band threshold method (SBT), reflectance difference threshold method (RDT), normalized difference snow index method (NDSI), modified normalized difference snow index method (MNDSI) and lake ice index method (LII), were selected to compare their accuracies in extracting lake ice extent by combining them with four evaluation metrics of accuracy, precision, recall and mean intersection over union (MIoU). In addition, the ability of the high-precision LII method for extracting long time series lake ice phenology and its applicability to multiple types of lakes were verified. The results showed that compared with the NDSI method, the other four methods more easily distinguished between lake ice and lake water by setting thresholds. The SBT method and the RDT method had better extraction effects in the freezing process and the melting process, respectively. Compared with the NDSI and MNDSI methods, the LII method showed a significant improvement in lake ice extraction over the entire freeze–thaw cycle, with the smallest mean monitoring error of 1.53% for the percentage of lake ice area in different periods. Meanwhile, the LII method can be used to determine long term lake ice phenology dates and had good performance in extracting lake ice for different types of lakes on the Qinghai–Tibet Plateau with the optimal threshold interval of 0.05~0.07, which can be used for lake ice monitoring and long-term phenological studies in this region.