The ‘Akizuki’ pear has become increasingly popular in China in recent years. However, the ‘Akizuki’ pear often suffers from severe rot diseases during the postharvest storage period. Those during storage have not been thoroughly elucidated In this study, fungal pathogens causing postharvest decay of ‘Akizuki’ pear were identified through multi-gene phylogenetic analysis, followed by assessment of the antifungal efficacy of chlorine dioxide (ClO₂) at varying concentrations. A total of 18 strains were isolated and identified as pathogens by Koch postulates. The isolated pathogens were taxonomically identified by combining morphological characterization of hyphae/spores with multi-gene phylogeny (ITS, β-tub, tef1). The results revealed that isolates A1-A11 were identified as Alternaria alternata, D1-D3 as Diaporthe eres, P1 as Penicillium citrinum, and P2-P4 as Penicillium expansum. The strain with the strongest pathogenicity in each genus was selected as the representative strain for subsequent control experiments. ClO₂ significantly inhibited the development of the D. eres, A. alternata, and P. expansum by suppressing mycelial growth and disrupting cell membrane structure of pathogens, in which the EC50 values were 35.56 mg/L, 24.71 mg/L, and 41.98 mg/L, respectively, showing comparable antifungal activity to conventional fungicides. This has clarified the occurrence and control of postharvest decay diseases of ‘Akizuki’ pear fruit and provided more options for the practical applications in postharvest disease control of pear fruits.