The invention discloses a preparation method of an artemisinin microcapsule, comprising: dissolving artemisinin in ethanol having the weight ratio of 6-8, adding sodium starch phosphate and a tween emulsifier, and stirring well to obtain a core solution; using chitosan, octadecyl quaternary ammonium salt of carboxymethyl chitosan and gelatin as a wall material, adding water 6-8 times as heavy as the wall material, heating to 50-60 DEG C, and stirring well to obtain a wall suspension; adding the core solution and the wall suspension into an ultrasonic homogenizer at the weight ratio of 1:(3-5)to perform homogenizing for 20-30 min to obtain an emulsion; delivering the emulsion to a granulating sprayer to perform spray drying, cooling to room temperature, and packaging to obtain the artemisinin microcapsule. The artemisinin microcapsule prepared herein can provide isolation of its effective ingredients with the outside and protect them from being influenced by heat sources, light sources, air and the like, stability of artemisinin is significantly improved, the shelf life is significantly extended, active ingredients of artemisinin can be well preserved, and processing, storing and transporting of artemisinin are facilitated.