Given the growing need for biofuel production but the lack of suitable land for producing biomass feedstock, development of stress-tolerant energy crops will be increasingly important. We used comparative transcriptomics to reveal differential responses to long-term salt stress among five populations of Miscanthus lutarioriparius grown in the natural habitats and salinity experimental site. A total of 59 genes were found to be potentially responsive to the high-salinity conditions shared by the five populations, including those involved in detoxification, plant defense, photosynthesis, and signal transduction. Of these genes, about 70% were related to abiotic stress response. Among five populations, the most contrasting performance between relatively high survival rates and the relatively weak growing traits was in accordance with the down-regulation of genes involved in growth and up-regulation of genes related to plant stress tolerance in one of the populations. These results might reveal a potential tolerance-productivity trade-off, where resources were allocated from growth to stress resistance. The comparative transcriptomics of different populations among different environments will provide a basis for breeding and domestication of energy crops.