Abstract: Microbes play crucial roles in a wide range of ecosystem functions and constitute a large proportion of Earth’s biodiversity. However, ecologists are yet to come to a consensus on the trends and underlying mechanisms of microbial species diversity along temperature gradients (e.g. across latitudes). I investigated the species richness pattern that merges in mesophilic bacterial communities assembled at different environmental temperatures using a general, metabolically-constrained mathematical model parameterized with real data. I find that species richness after assembly declines with increasing temperature, irrespective of the strategies that microbes adopt. This decline with warming is mainly governed by differential extinction of species’ metabolic strategies driven by resource competition in the face of changing temperature. Specifically, species with higher intrinsic carbon use efficiencies (CUE) are favoured especially at higher temperatures, which is the combination of higher thermal sensitivities in uptake rate and lower thermal sensitivities in respiration rates. As metabolic rates increase exponentially with temperature, effective competition among species increased for the fixed amount of resources available, so relatively higher facilitation and higher resources partitions (lower resource overlaps) are favoured. These results suggest that even if the species thermal physiologies vary independently, the emergent community CUE would still increase with temperature as a result of species sorting. To the best of my knowledge, this is the first theoretical study on the effect of temperature on diversity and its link with CUE of complex microbial communities. This study provides new mechanistic insights into the geographical patterns of microbial diversity and their relation to carbon cycling.