The Mekong River Basin (MRB) has experienced drastic and extensive land-use and land-cover changes (LULCCs) since the 1990s, including the conflicts between cropland and forest, yet remain quantitatively uninvestigated. With three decades (1990–2020) of land-use products, here we reveal the characteristics of LULCCs and the conflicts between cropland and forest in the MRB and its three sub-basins, i.e., upstream area (UA), midstream area (MA), and downstream area (DA). The four main results are as follows: (1) Since 1990, the dominated features are forest loss and cropland expansion in the MRB and show obvious sub-basin differences. (2) The LULCC was most active before 2000, with a comprehensive dynamic degree of almost 2%. Among them, construction land has the highest single dynamic degree (5%), especially in the DA, reaching 12%. (3) The key features of land-use transfer are the interconversions of forest and cropland, as well as cropland converted into construction land. About 18% (63,940 km2) of forest was reclaimed as cropland, and 17% (45,967 km2) of cropland was returned to forest in the past 31 years. (4) The conflict between cropland and forest was the most dominant LULCC, accounting for 86% of the MRB area. Overall, cropland expansion and forest loss (CEFL) were more dominant in the DA, while cropland fallow and forest restoration (CFFR) had an advantage in the MA. Indeed, CEFL was mainly seen in the plains below a 200 m elevation level, while CFFR tended to occur in the highlands. Our basin-scale study can enrich the existing pan-regional results of LULCCs, and facilitates the understanding of the dynamics and related mechanisms of CFER and CFFR in the tropics.