This study was undertaken to increase the biomass and carbohydrate productivities of a freshwater cyanobacterium Synechococcus elongatus under hot outdoor conditions through genetic manipulation to facilitate the application of using the cyanobacterial biomass as bio-refinery feedstocks. The stress tolerance genes (hspA, osmotin) were expressed in S. elongatus to improve their growth under various environment stresses of outdoor cultivation. The results revealed that over-expression of hspA and osmotin significantly improved temperature (45 °C), high light intensity, and salt tolerances of S. elongatus cells, making it capable of efficiently growing in seawater under outdoor cultivation. The carbohydrate productivity of these stress tolerant strains was also 15–30-fold higher than that of the control strain, although the carbohydrate contents of the recombinant and control strains were similar. Our findings demonstrate that the genetic engineering for improved stresses tolerance in S. elongatus could facilitate the feasibility of using cyanobacteria as feedstock for bio-refinery industry.