Recently released Moderate-Resolution Imaging Spectroradiometer (MODIS) land surface temperature (LST) collection 6.1 (C6.1) products are useful for understanding ice–atmosphere interactions over East Antarctica, but their accuracy should be known prior to application. This study assessed Level 2 and Level 3 MODIS C6.1 LST products (MxD11_L2 and MxD11C1) in comparison with the radiance-derived in situ LSTs from 12 weather stations. Significant cloud-related issues were identified in both LST products. By utilizing a stricter filter based on automatic weather station cloud data, despite losing 29.4% of the data, accuracy of MODIS LST was greatly improved. The cloud-screened MODIS LST exhibited cold biases (−5.18 to −0.07°C, and root mean square errors from 2.37 to 6.28°C) than in situ LSTs at most stations, with smaller cold biases at inland stations, but larger ones at coastal regions and the edge of plateau. The accuracy was notably higher during warm periods (October–March) than during cold periods (April–September). The cloud-screened MODIS C6.1 LST did not show significant improvements over C5 (Collection 5) version across East Antarctica. Ice-crystal precipitation occurring during temperature inversions at the surface (Tair-Tsurface) played a crucial role in MODIS LST accuracy on inland plateau. In coastal regions, larger MODIS LST biases were observed when the original measurements were lower.