•TTO alters the morphology and ultrastructure of mitochondria in B. cinerea.•TTO decreases intracellular ATP content and increases extracellular ATP content.•TTO causes mitochondria dysfunction and disrupts the TCA cycle in B. cinerea.•Relative ROS levels are increased by TTO treatment. In order to investigate the effects of tea tree oil (TTO) on mitochondrial morphology and function in Botrytis cinerea, mycelia were treated with TTO at different concentrations. TTO at 2ml/l severely damaged mitochondria, resulting in matrix loss and increased mitochondrial irregularity. Mitochondrial membrane permeability was increased by TTO, as evidenced by a decrease in intracellular adenosine triphosphate (ATP) content and an increase in extracellular ATP content. Increasing concentrations of TTO decreased the activities of enzymes related to mitochondrial function and the tricarboxylic acid (TCA) cycle, affecting malic dehydrogenase, succinate dehydrogenase, ATPase, citrate synthetase, isocitrate dehydrogenase and α-ketoglutarate dehydrogenase, while sharply increasing the level of reactive oxygen species (ROS). These results suggest that mitochondrial damage, resulting in the disruption of the TCA cycle and accumulation of ROS, is involved in the mechanism of TTO antifungal activity against B. cinerea.