To explore the effect of magnetic treatments on the soil fertility and health, the soil biological properties in the rhizosphere of peas were analyzed using pot culture. Five treatments, i.e. No-treatment (CK), iron powder (A), magnetized iron powder (B), magnetized iron powder+0.2 T magnet (C) and 0.2 T magnet treatments (D) were set for analyzing with the high-throughput sequencing technique. The amounts of cultivable bacterial and fungi could be significantly increased by treatment C. Meanwhile, compared to CK, the biomass C, N, P and the activities of β-Glucosidase, Aminopeptidase and Phosphatase were also increased by 34.0%, 46.0%, 44.2% and 24.6%, 23.7%, 31.8% compared to treatment C, respectively. In addition, the indexes of richness and diversity of bacteria, such as Ace, Chao1 and Shannon in treatment C were also significantly higher than those in CK. Moreover, Sneathiella, Desulfurispora and nannocystaceae were the unique bacteria in CK under genus level, but seven different bacterial groups under genus level were showed in treatments A and B. Eleven different bacterial groups were presented in treatment C. And there were only eight different bacterial groups in treatment D. In summary, the biological indicators of soil fertility and health, such as soil cultivable microorganisms, microbial biomass, enzyme activities and bacteria diversity were all significantly improved under treatment C, which used 0.2 T magnet + 5 g magnetized iron powder. It indicated that the soil fertility and ability to resist soil-borne diseases could be promoted by treatment.