Abstract: We conducted a field experiment to evaluate the effects of rotation system and bioorganic manure on soil microbial characteristics of Chrysanthemum cropping system. Taking Chrysanthemum morifolium Ramat and wheat as experimental plants, treatments under Chrysanthemum continuous cropping system (M₁), conventional Chrysanthemumwheat rotation system (M₂), and Chrysanthemumwheat rotation system receiving bio-organic manure application of 200 kg·667 m^-2 (M₃) were designed. Soil chemical properties, soil microbial biomass carbon (MBC) and nitrogen (MBN), and the amounts of different types of soil microorganisms were determined. Results showed that compared with M₁, treatments of M₂ and M₃ significantly increased soil pH, organic matter, available N, P, and K, MBC, MBN, and the amounts of bacteria, fungi and actinomycetes, but decreased the ratio of MBC/MBN, and the relative percentage of fungi in the total amount of microorganisms. Treatment of M3 had the highest contents of soil organic matter, available N, available P, available K, MBC, MBN, and the amounts of bacteria, fungi and actinomycetes, with the values being 15.62 g·kg^-1, 64.75 mg·kg^-1, 83.26 mg·kg^-1, 96.72 mg·kg^-1, 217.40 mg·kg^-1, 38.41 mg·kg^-1, 22.31×10⁶ cfu·g^-1, 56.36×10³ cfu·g^-1, 15.90×10⁵  cfu·g^-1, respectively. We concluded that rational crop rotation and bioorganic manure application could weaken soil acidification, improve soil fertility and microbial community structure, increase the efficiency of nutrition supply, and have a positive effect on reducing the obstacles of continuous cropping.