The invention provides an efficient breeding method of purple potato tissue culture seedlings. The efficient breeding method of the purple potato tissue culture seedlings comprises the following steps of treating purple potato tubers at ultralow temperature; performing induced culture on root tips and stem tips of seed potatoes; performing rooting culture on strong seedlings, and conducting virus detection on test-tube plantlets; performing induced culture and virus detection on miniature potatoes; performing transplanting and cuttage grafting breeding on the miniature potatoes. According to the efficient breeding method of the purple potato tissue culture seedlings, provided by the invention, miniature potato seedlings are bred by adopting virus eradication of stem tips and root tips; the culture cycle of the root tips is different from that of the stem tips; the root tips and the stem tips are jointly cultured, so that the time cost can be effectively reduced, seed potato resources are fully and efficiently utilized, and further the reproduction cost of the tissue culture seedlings is reduced; besides, the test-tube plantlets cultured by using the root tips are high in reproduction speed, so that the working efficiency is improved, and the production cost is reduced.