The invention discloses an FISH probe set for detecting FGFR2 fusion and application thereof. The probe set comprises a 5' end probe set and a 3' end probe set; the 5' end probe set adopts BAC of a nucleotide of one side of an FGFR2 gene telomere as a template through cloning and is obtained by amplifying random primers, and each probe is modified with a first reporter group; the 3' end probe setis obtained by cloning the BAC of the nucleotide sequence of the centromere side of the FGFR2 gene into a template and amplifying the random primers, and each probe is modified with a second reportergroup. The set has the advantages of rapid and simple operation, accurate and reliable detection result and accurate detection of all fusion types of the FGFR2 gene, provides a reference for the treatment of intrahepatic cholangiocarcinoma patients, is beneficial to individualized targeted therapy of the patients, reduces drug side effects, improves patient survival quality, reduces the burden onfamilies and society, and is suitable for large-scale promotion and application.