The use of Remote Sensing (RS) data is crucial for promptly detecting and monitoring changes in both short and long term, providing real time information on Land Use/Cover (LULC), Land Surface Temperature (LST), and Enhanced Vegetation Index (EVI), adapting spatio-temporal variations. The primary focus of this study is to assess the effect of LULC changes on LST in Tashk-Bakhtegan and Maharloo (TBM) lakes basin, Iran, within 2001, 2011, and 2021, using MODIS data. Specifically, five main LULC classes involving: water body, rangeland, cropland, urban area, and bareland were identified. Beside accuracy and transition of LULC maps using User Accuracy (UA), Producer Accuracy (PA), and Kappa Coefficient (KC), the analysis included changes in LULC, Enhanced Vegetation Index (EVI), and LST, as well as the relationship among them when vegetation cover was at its peak. Moreover, a one-way analysis of variance (ANOVA) test was performed to group these variables using Duncan's test. The results showed that the accuracy of LULC maps were more than 84% for all the years. Furthermore, the conversion of croplands to rangelands showed the most significant changes, with a total of 1311.38 km2 during 2001–2021. Average EVI remained almost stable across the total area, whereas average LST generally increased by 0.65 °C. Barelands consistently exhibited the highest temperatures in all the years, followed by urban areas. While no significant changes were observed in the EVI averages, significant changes were observed in the LST across all LULC classes in different years. The results also indicated a consistent negative correlation between LST and EVI, stronger in croplands than rangelands, with Spearman's correlation coefficient of −0.714, −0.674, and −0.623 over the total area in 2001, 2011, and 2021, respectively. The findings are crucial for land planners to comprehend the effects of LULC changes on LST to adopt appropriate strategies in the TBM lakes basin.