Mutation breeding through irradiation has been applied to several varieties and genetic resources since the discovery of the use of X-rays for inducing mutations in plants by Stadler in 1928. A heavy ion beam with high linear energy transfer (LET) shows a higher relative biological effectiveness (RBE), and it is more effective in inducing plant mutations than low LET radiations, such as X-rays, gamma rays, and electrons. Since early 1990s, several plant breeding programs in Japan have used heavy ion beams from accelerators. These beams impart a high energy effect on a local target; therefore, they induce a higher number of single and double strand DNA breaks. In addition, they induce a large number of DNA deletions than low LET radiations. Therefore, a heavy ion beam is superior to low LET radiations in terms of induction rate and the mutation spectrum. In Korea, a heavy ion accelerator that can be used for breeding is under construction. However, a large-capacity proton accelerator (KOMAC: Korea Multi-purpose Accelerator Complex) was built recently, and it is a pioneer step in breeding research worldwide. This review summarizes the basic characteristics, successful research achievements, and the prospect of application of high LET accelerator beams in plant mutation breeding.