This study investigated the effect of heat treatment on the vitality and pathogenicity of citrus pathogenic fungi after harvest. The vitality of the fungi was tested by heat-treatment of the fungal spore suspension as well as fungal spore suspension with navel orange skin at 52 ± 1 ℃ for 10 min. Fungal spore viability indices, such as the mortality, morphology, suspension supernatant conductivity value, and OD260nm of five strains of fungus (marked A, B, C, D, and E) were examined after the two heat treatments, respectively. The pathogenicity of strain A (as an example) was determined by analyzing and comparing the changes in disease incidence in navel oranges, caused by contamination with fungal spores heat treated with or without navel orange skin. The results of these analyses revealed that heat-treatment without orange skins resulted in a decrease in fungal spore vitality, while not affecting its pathogenicity. However, simultaneous heat and navel orange peel treatment caused great structural damage to the pathological fungal spores, affecting a significant decrease in its vitality and pathogenicity, compared to fungal spores that were only subjected to heat-treatment. The mortality of strain A spores increased from 48% to 72%; in addition, the emergence time of typical disease lesions in navel oranges was delayed from 4 days to over 7 days.