The biocontrol efficacy of Rhodotorula mucilaginosa against postharvest diseases of strawberries can be significantly enhanced by chitosan-inducing incubation. But the molecular mechanisms involved in the enhanced biocontrol efficacy of R. mucilaginosa was not explored comprehensively. In recent years, the rise of transcriptome has provided favorable conditions for the exploration of the molecular mechanisms in various fields. From the transcriptome and bioinformatics analysis, the expression of some DEGs related to growth and reproduction, adhesion, antioxidant capacity of R. mucilaginosa were up-regulated. These results provided a theoretical reference for further study of the molecular mechanisms involved in enhancing biocontrol efficacy of antagonistic yeast incubated with elicitor molecule and would provide a theoretical basis to accelerate the application process of antagonistic yeast.