Thiopurine is one type of common chemotherapy drugs for the treatment of acute lymphoblastic leukemia (ALL) during remission. It must be metabolized and transformed to thioguanine nucleotides in vivo, which have the biological activity for killing tumor cells. Once key enzymes in thiopurine metabolic pathway develop single nucleotide polymorphisms or functional mutations, tumor cells will become resistant to thiopurine treatment and relapse will occur quickly. This article summarizes research progresses of metabolic enzyme mutations, which contribute to the thiopurine resistance in ALL, in order to provide novel ideas and strategies for overcoming the thiopurine resistance.