The invention discloses purple sweet potato and vanilla flavored sandwiched wafer biscuits and a preparation method thereof. The purple sweet potato and vanilla flavored sandwiched wafer biscuits are prepared from cookie pieces and a stuffing, wherein the cookie pieces are mainly prepared from wheatmeal, purple sweet potato powder, rice flour, wheat starches, lotus leaf powder and radix puerariae powder; scutellaria baicalensis powder, radix polygonati officinalis powder and lily powder are added into the stuffing. The preparation method comprises the following steps: pretreating the raw materials, pulping and baking the cookie piece raw materials, preparing and molding the stuffing, and the like. Ingredients of the conventional wafer biscuits are changed, and various components are added, so that the taste is delicious. The purple sweet potatoes are added in the raw materials, and are enriched with proteins, starches, pectin, cellulose, amino acid, vitamins and various minerals, and selenium elements and anthocyanin, so that the wafer biscuits have the effects of resisting the cancer and protecting the health; by the adding of the scutellaria baicalensis powder, the radix polygonati officinalis powder and the lily powder, the wafer biscuits have extremely high medical value, so that the immunity of a human body is enhanced, and the nutritional health protection effect is good. The wafer biscuits are a bakery product integrating nutrition, leisure and health protection, and taste good; the preparation method is simple and convenient, and can realize batch production on an automatic production line.