The invention relates to embedded nano iron/microbe microspheres and a preparation method thereof. The embedded nano iron/microbe microspheres are formed under the gelation action of calcium alginate. An embedding method is adopted in the prepared nano iron/microbial microspheres; nano iron and microbe are immobilized in the microspheres together by using the cross-linking and curing effects of a sodium alginate embedding agent and a calcium chloride cross linker; and the prepared microspheres have uniform particle size distribution, small average particle size and large specific surface area, and can be widely applied in the fields of environmental pollution treatment and environmental remediation.