The invention discloses a 2,5-dichlorotoluene isomerization catalyst as well as a preparation method and application thereof. The 2,5-dichlorotoluene isomerization catalyst is prepared from 0.01 to 2.0 weight percent of VIII group metals (metered by taking a dry carrier as a reference) and a composite carrier, wherein the composite carrier is prepared from 10 to 80 weight percent of mordenite, 10 to 80 weight percent of EU-1 zeolite and 10 to 50 weight percent of aluminum oxide. The 2,5-dichlorotoluene isomerization catalyst disclosed by the invention is specifically suitable for raw materials containing 2,5-dichlorotoluene for carrying out isomerization reaction to generate 2,4-dichlorotoluene and 2,6-dichlorotoluene, and higher conversion activity and higher selectivity are obtained.