The invention provides a hydrate of an ilaprazole salt and a preparation method thereof. The hydrate is shown by a formula (I), wherein M is Li, Na or K, n is equal to 1, and x is equal to 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4 and 4.5 or M is Ca, Mg or Zn, n is equal to 2 and x is equal to 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4 and 4.5. The invention also provides application of the hydrate of the ilaprazole salt. Compared with ilaprazole and a salt thereof, the hydrate of the ilaprazole salt can be used as a proton pump inhibitor for treating diseases relevant with disorder in gastric acid secretion, has low side effect, and can be developed to form new clinically-acceptable medicaments. Simultaneously, the preparation method is simple and easy, and repeated experiments prove that the hydrate of the ilaprazole salt has a stable process and can be used for industrial production.