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In this study, we assessed the performance of 34 Coupled Model Intercomparison Project Phase 5 (CMIP5) general climate models (GCMs) for simulating the observed temperature over the Lower Mekong Basin (LMB) in 1961-2004. An improved score-based method was used to rank the performance of the GCMs over the LMB. Two methods of multi-model ensemble (MME), sub-ensemble from the top 25% ranked GCMs and full ensemble from the entire GCMs, were calculated using arithmetic mean (AM) method and downscaled using the Delta method to project future temperature change during two future time periods, the near future (2006-2049) and the far future (2050-2093), under representative concentration pathways (RCP2.6, RCP4.5, and RCP8.5 scenarios) over the LMB. The improved score-based method combining multiple criteria showed a robust assessment of the GCMs performance over the LMB, which can provide good information for projecting future temperature change. The results showed a significant increase in temperature over the LMB under the two ensembles. However, there were differences in the magnitudes of the future temperature increase between the two ensemble methods, with a higher mean annual temperature increase from full ensemble and sub-ensemble at 1.26 degrees C (1.09 degrees C), 1.90 degrees C (1.70 degrees C), and 2.97 degrees C (2.78 degrees C) during 2050-2093 under the RCP2.6, RCP4.5, and RCP8.5 scenarios compared to the values at 0.93 degrees C (0.87 degrees C), 0.99 degrees C (0.95 degrees C), and 1.09 degrees C (1.06 degrees C) during 2006-2049, respectively, relative to the reference time period of 1961-2004. In the future (2006-2093), the temperature is likely to increase at 0.06 degrees C, 0.18 degrees C, and 0.39 degrees C decade(-1) under the RCP2.6, RCP4.5, and RCP8.5 scenarios by the sub-ensemble, while a higher temperature increase at 0.08 degrees C, 0.20 degrees C, and 0.42 degrees C was found by the full ensemble over the LMB, relative to the reference time period of 1961-2004. On the whole, the higher warming mainly occurred in the northern and central areas over the LMB, while the lower warming mainly occurred in the southeast and the southwest, especially under the RCP4.5 and RCP8.5 scenarios, with the warming increased with increasing RCP for both ensembles. Moreover, in order to reduce the uncertainty of temperature projection in further studies in the LMB, multiple methods of GCMs ensemble should be considered and compared.