Varied environmental stress can affect cell growth and activity of the cellular catalyst. Traditional path of adaptive evolution generally takes a long time to achieve a tolerance phenotype, meanwhile, it is a challenge to dissect the underlying genetic mechanism. Here, using SCRaMbLE, a genome scale tool to generate random structural variations, a total of 222 evolved yeast strains with enhanced environmental tolerances were obtained in haploid or diploid yeasts containing six synthetic chromosomes. Whole genome sequencing of the evolved strains revealed that these strains generated different structural variants. Notably, by phenotypic-genotypic analysis of the SCRaMbLEd strains, we find that a deletion of gene YFR009W (GCN20) can improve salt tolerance of Saccharomyces cerevisiae, and a deletion of gene YER056C can improve 5-flucytosine tolerance of Saccharomyces cerevisiae. This study shows applications of SCRaMbLE to accelerate phenotypic evolution for varied environmental stress and to explore relationships between structural variations and evolved phenotypes.