The invention discloses a method for producing virus-free atractylodes macrocephala koidz seedlings. The method comprises the following steps: 1, pre-treating atractylodes macrocephala koidz seeds and aseptically sprouting the embryos atractylodes macrocephala koidz seeds, to be specific, inoculating atractylodes macrocephala koidz embryos into a primary culture medium comprising 1/2MS, 20g/L sucrose and 6g/L agar powder; 2, performing proliferation culture, wherein a proliferation culture medium comprises MS, 1.0mg/L 6-BA, 0.2mg/L NAA, 30g/L sucrose and 6g/L agar powder; 3, detecting viruses, to be specific, rejecting virus-containing atractylodes macrocephala koidz seedlings, and continuing to perform proliferation culture on the virus-free atractylodes macrocephala koidz seedlings; 4, performing rooting culture, to be specific, uprightly inserting rootless atractylodes macrocephala koidz tissue culture seedlings which are cultured to about 4cm into a rooting culture medium comprising 1/2MS, 1.0mg/L NAA, 20g/L sucrose and 6g/L agar powder; 5, performing acclimatization and transplantation. According to the method, the formulae of the primary culture medium and the rooting culture medium for atractylodes macrocephala koidz are obtained by single-factor tests, the formula of the proliferation culture medium for the atractylodes macrocephala koidz tissue culture seedlings is obtained by an orthogonal design, and most importantly, the virus-free atractylodes macrocephala koidz seedlings are obtained in an embryo culturing way by utilizing the fact that embryo parts are virus-free.