The effects of different concentrations of chitin on the activity of enzymes and fungal communities existing in replant soils were explored, for enrichment of soils to alleviate apple replant disease (ARD). In this study, Malus hupehensis Rehd. seedlings potted in replant soil were treated with four concentrations of chitin (0, 0.5, 1.0, and 2.5 g/kg). The growth of seedlings was monitored though plant height, fresh and dry weight, antioxidant enzyme activities, such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and lipid peroxidation in roots. Simultaneously, soil enzyme activities, soil microbial load, and fungal community structure, which was measured by terminal-restriction fragment length polymorphism (T-RFLP) profiles, were determined in soil samples subjected to the four chitin treatments. Compared with the control, seedlings treated with 1.0 g/kg chitin showed 36.8%, and 82.1% and 100.8% increase in plant height, and fresh and dry weight, respectively. The optimal dose of chitin could increase antioxidant enzyme activity in the root system of the seedlings, whereas high doses inhibited enzyme activity. The effectiveness of chitin treatment for inhibiting the activity of SOD, POD, and CAT in the root system of M. hupehensis seedlings decreased in the following order:1.0 g/kg > 0.5 g/kg > 0 g/kg > 2.5 g/kg. Chitin treatment at 1.0 g/kg enhanced the bacterial-fungal ratio, and resulted in a "bacteria-rich soil"; consequently, sucrase, urease, protease, phosphatase, catalase, and polyphenol oxidase activities increased by 8.6%, 40.5%, 81.1%, 15.3%, 18.7%, and 49.8%, respectively. Remarkable differences in T-RFLP profiles were observed among control, 0.5 g/kg, 1.0 g/kg, and 2.5 g/kg treatments. A significant difference in fungal community structure was observed with the application of different doses of chitin. The Shannon diversity, evenness, and richness indexes were the highest in replanted soil treated with 1.0 g/kg chitin and the least in soil treated with 2.5 g/kg chitin. Principal component analysis indicated that fungal community structure of soil treated with 1.0 g/kg chitin was considerably different from that of the control soil and soil treated with 2.5 g/kg chitin. The present study showed that low concentrations of chitin could alleviate ARD stress in M. hupehensis Rehd. seedlings, whereas high concentrations could aggravate ARD stress. Collectively, these findings suggest that chitin applied to replant soil at 1.0 g/kg obviously enhanced plant height, fresh and dry weight, improved the soil environment, and effectively alleviate ARD stress in M. hupehensis Rehd. seedlings, therefore, a chitin dose of 1.0 g/kg was considered optimal for replant soil.