There is provided a method for etching magnetic tunnel junction, using an etching apparatus including a sample loading chamber, a vacuum transition chamber, a reactive ion plasma etching chamber, an ion beam etching chamber, a coating chamber, and a vacuum transmission chamber. The method completes the etching of the magnetic tunnel junction in the reactive ion plasma etching chamber, performs ion beam cleaning in the ion beam etching chamber, and performs coating protection in the coating chamber. The transmission among the respective chambers is all in a vacuum state. The invention can overcome the bottleneck in the production of high-density small devices, while greatly improving the yield, reliability and production efficiency of the devices.