Our previous study demonstrated that the combined application with oligochitosan (OCH) improved the biocontrol efficacy of Pichia caribbica against postharvest black spot of tomato fruits. The involved mechanisms were elucidated based on the induction of fruit resistance. However, the mechanisms needed to be further explored from the antagonistic yeast perspective. The current study determined the effects of OCH on P. caribbica growth in vitro and the effects of combined application with OCH on the colonization ability, the reactive oxygen species (ROS) accumulation, especially the gene expression levels of P. caribbica in fruit wounds. The findings revealed that OCH increased the viable cell number of P. caribbica in NYDB and in tomato fruit wounds. Additionally, combined application with OCH could alleviate ROS accumulation in P. caribbica inoculated in fruit wounds. Transcriptome analysis revealed that the genes related to MAPK signal transduction, meiosis – yeast, DNA replication, tryptophan metabolism and glutathione metabolism of P. caribbica were induced by the combined application with OCH in fruit wounds, which triggered its MAPK signal transduction, promoted its growth and reproduction, and improved its antioxidant capability. Therefore, the capability of P. caribbica to survive and colonize fruit wounds were raised and its antagonistic efficacy against postharvest black spot pathogen was heightened by combined application with OCH. This study will open up new possibilities for improving the biocontrol efficacy of antagonists against postharvest pathogens of fruits and vegetables.