β-Cyclocitric acid (β-CCA) is a bioactive apocarotenoid previously shown to improve drought tolerance in annual plants. However, the underlying molecular mechanism of this process remains largely elusive. Moreover, the question about the activity of β-CCA in perennial fruit crops is still open. Here, we found the treatment of β-CCA to enhance drought tolerance in peach seedlings. The application of β-CCA significantly increased the relative water content and root activity, and reduced the electrolyte leakage of peach seedlings under drought stress. Moreover, treatment with β-CCA under drought stress increased chlorophyll fluorescence, indicating a positive effect on photosynthesis, while also enhancing superoxide dismutase and peroxidase activity, and reducing ROS levels. Consistent with these alterations, transcriptome analysis revealed an up-regulation of photosynthesis and antioxidant-related genes upon the application of β-CCA under drought stress. We also detected an induction in genes related to detoxification, environmental adaptation, primary metabolism, phytohormone, phenylpropanoid, and the biosynthesis of cutin, suberine and wax, which might contribute to the induction of drought resistance. Altogether, our study reveals that β-CCA positively modulates peach drought tolerance, which is mainly mediated by enhancing photosynthesis and reducing ROS, indicating the potential of utilizing β-CCA for drought control in peach and perhaps other fruit crops.