Objective: This study aimed to elucidate the temporal characteristics, physiological responses and interactive relationships of Penicillium pathogens in Gonggan mandarin (Citrus reticulata 'Gonggan') fruits, thereby providing a theoretical basis for targeted preservation technologies. Methods: Experiment 1 involved observing storage diseases in Gonggan mandarin fruits, while experiment 2 focused on the physiological responses of the fruits to Penicillium inoculation. In the Penicillium inoculation experiment, three major pathogenic fungi—Penicillium digitatum (Pd), P. italicum (Pi), and P. expansum (Pe)—were isolated and identified from Gonggan mandarin fruits in the Xijiang River Basin of Guangdong Province and used as pathogen material. A total of seven treatments were set up, including single and combined inoculations, along with two control groups (CK1: Fruits immersed in 0.1% NaClO solution for 3 min; CK2: Peel wounded but not inoculated). Disease symptoms were dynamically observed, incidence rate (IR) and disease index (DI) were statistically calculated, fruit storage quality was analyzed, reactive oxygen species metabolism indicators and defense enzyme activities were measured, and a disease-physiology regression model was constructed. Results: During the storage of Gonggan mandarin fruits, green mold was the predominant disease, exhibiting a higher severity than blue mold, with complex infections being commonly observed. In single inoculation treatments, Pi and Pe developed symptoms earlier, but Pd exhibited faster spread and stronger infectivity, with a significantly higher incidence rate (IR) than Pi and Pe just 4 days after inoculation. Following combined inoculation, the DI of the triple mixed inoculation (Pd+Pi+Pe) was lower than that of the (Pd+Pi) combination (P<0.05), indicating that interspecific competition among Penicillium species significantly delayed disease progression. Fruit injury significantly promoted quality deterioration in Gonggan mandarin fruits, resulting in a substantial increase in weight loss rate, and it also induced H₂O₂ accumulation and a significant rise in CAT activity (P<0.05). Pathogen infection induced severe oxidative stress and a disrupted defense enzyme system in Gonggan mandarin fruits, which was manifested by a substantial increase in the generation rate of O₂⁻· and the contents of H₂O₂ and malondialdehyde (MDA); In contrast, the activities of phenylalanine ammonia-lyase (PAL) and catalase (CAT) were significantly inhibited, exhibiting a highly significant negative correlation with disease severity indices IR and DI (P<0.01). Conclusion: During the storage of Gonggan mandarin, green mold was the dominant disease, often accompanied by complex infections. Mechanical damage accelerated fruit decay by facilitating the infection of Penicillium spp. As the predominant pathogen, Penicillium digitatum drove oxidative damage and quality deterioration in the fruit through sustained suppression of PAL activity and induction of CAT activity collapse. Moreover, interspecific competition among Penicillium species mitigated disease development in Gonggan mandarin.