(1) Background: Organic food produced in environmentally friendly farming systems has become increasingly popular. (2) Methods: We used a DNA metabarcoding approach to investigate the differences in the microbial community between organic and conventional ‘Huangguan’ pear fruit; and (3) Results: Compared to a conventional orchard, the fruit firmness in the organic orchard had significantly lowered after 30 days of shelf-life storage at 25 °C, and the soluble solids content (SSC), titratable acid (TA), and decay index were higher. There were differences in the microbial diversity between organic and conventional orchards pears. After 30 days of storage,FusariumandStarmerellabecame the main epiphytic fungi in organic fruits, whileMeyerozymawas dominant in conventional fruits.Gluconobacter,Acetobacter, andKomagataeibacterwere dominant epiphytic bacteria on pears from both organic and conventional orchards after a 30-day storage period.Bacteroides,Muribaculaceae, andNesterenkoniawere the main endophytic bacteria throughout storage. There was a negative correlation between fruit firmness and decay index. Moreover, the abundance ofAcetobacterandStarmerellawere positively correlated with fruit firmness, whileMuribaculaceaewas negatively correlated, implying that these three microorganisms may be associated with the postharvest decay of organic fruit; (4) Conclusions: The difference in postharvest quality and decay in organic and conventional fruits could potentially be attributed to the variation in the microbial community during storage.