Green mold caused by Penicillium digitatum is a common disease of postharvest citrus. Exploring its pathogenesis will contribute to the research and development of efficient and safe postharvest biological control methods for citrus. In this study, gas chromatography-mass spectrometry (GC-MS) and liquid chromatograph-mass spectrometer (LC-MS) were used to analyze the metabonomics of Citrus reticulata Blanco wound before and after P. digitatum infection. The results showed that the metabolites such as carbohydrates, esters, organic acids, and resistance-inducing substances changed dramatically in the citrus wound after infection with P. digitatum. In addition, in combination with previous results from physiological experiments and transcriptome analysis of P. digitatum before and after infection, we revealed the important changes of energy metabolism, protein hydrolysis process and defense response in the citrus wound after infection with P. digitatum and discussed the pathogenesis and mechanism of green mold disease after citrus harvest. From this study, we provided new insights into the mechanism of P. digitatum infection in postharvest citrus, which laid a certain foundation for the formulation of new control strategies.