Chalcones are a class of flavonoids possessing a variety of biological activities, including antimicrobial and antioxidant effects. Therefore, chalcones and their derivatives have potential use in the control of postharvest diseases. In this work, the effects of 2ʹ,4ʹ-dichloro-chalcone on the in vitro growth and in vivo pathogenicity of F. tricinctum and T. roseum were investigated. The results showed that 100 µM of 2ʹ,4ʹ-dichloro-chalcone strongly inhibited mycelial growth and conidial production of F. tricinctum (32.3%) and T. roseum (65.2%) in vitro. This treatment also significantly inhibited the expansion of potato dry rot from F. tricinctum (48.6%) and apple rot spot from T. roseum (36.2%). The incubation of F. tricinctum and T. roseum conidia with this agent for 2 h increased their cell membrane permeability by 25% and 22.5%, respectively and conidial membrane permeability by 41.7 and 65.4%, respectively. This treatment also significantly inhibited the total respiration rate and activated the cyanide-resistant respiratory pathway in both pathogens. Protein immunoblotting showed that the treatment increased alternative oxidase (AOX) levels after 4 h in F. tricinctum and T. roseum by 52.76% and 39.13%, respectively. Conclusion: 100 µM 2ʹ,4ʹ-dichloro-chalcone significantly inhibited mycelial growth and spore production in F. tricinctum and T. roseum in vitro and reduced their pathogenicity in postharvest potato and apple crops. Further analysis indicated that 2ʹ,4ʹ-dichloro-chalcone disrupted the integrity of cell membranes and the mitochondrial respiratory electron transport chain which leaded to ROS burst and oxidative stress, AOXs were induced directly or indirectly, and the cyanide resistant respiratory pathway was activated. The in vitro growth and pathogenicity of F. tricinctum and T. roseum were inhibited.