In this study, we examined the effects of dazomet fumigation with different concentrations (0, 0.1, 0.2, 0.4 g·kg-1) on the microbial characteristics of continuous cropping soil and growth of Malus hupehensis seedling in greenhouse and open-field pot. The results showed that all the treatment of dazomet fumigation could promote the growth of M. hupehensis seedlings in continuous cropping soil, with 0.2 g·kg-1 treatment showing the strongest effect. Compared to the control, plant height, stem diameter, dry weight of M. hupehensis seedlings in 0.2 g·kg-1 dazomet fumigation were increased by 192.9% and 91.8%, 72.8% and 60.1%, 196.8% and 195.0%, 138.5% and 130.7%, respectively in greenhouse and open-field. The root related indices (root length, root area, root volume, root respiration rate) were significantly promoted. The activities of SOD, POD, CAT in roots were increased by 114.6% and 118.5%, 123.5% and 107.6%, 164.6% and 175.6% respectively compared with the control, whereas the content of malondialdehyde was significantly lowered. Soil bacterial content, fungal content, copy number of Fusarium oxysporum gene and soil enzyme activity were significantly decreased with the increasing dazomet concentrations. In conclusion, 0.2 g·kg-1 dazomet fumigation could increase the biomass of M. hupehensis seedlings in continuous cropping, improve soil environment, and effectively alleviate the continuous cropping obstacle. Therefore, 0.2 g ·kg-1 dazomet fumigation could be given priority during the reconstruction of old apple orchards.