d-limonene is a common natural flavor additive in food industry. Meanwhile, it can also inhibit the opportunistic pathogens Candida tropicalis by disrupting the relative balance of cell phenotypic parameters, but the molecular mechanism is still unclear. Therefore, this study attempted to reveal the molecular mechanism by integrated transcriptome and phenotypic parameters. The results suggested that d-limonene disrupted the biosynthesis of cell wall and membrane, the transcription of genes encoding key enzymes in glycolysis pathway, tricarboxylic acid cycle and oxidative phosphorylation pathway, and the proper folding of nascent protein in endoplasmic reticulum of Candida tropicalis, and thus damaged the integrity of cell wall and membrane, reduced the supply of NADH + H+ and FADH2 substrate-level for oxidative phosphorylation and ATP production, and increased the endoplasmic reticulum stress and unfolded protein response, which resulted in metabolic disorder of Candida tropicalis, including shrinkage and adhesiveness of cell morphology, permeabilization and depolarization of cellular and mitochondrial membrane, decrease of mitochondrial ATP, and increase of endogenous reactive oxygen species. These findings will facilitate a better understanding of anti-C. tropicalis mechanisms of d-limonene, as well as provide further insights into its potential applications in food preservation and preventive medicine.