Gastrointestinal stromal tumors(GIST) are known for their molecular alterations in KIT or PDGFR genes, and have become the paradigm of molecularly targeted therapies for solid tumors. Recent researches of genotype and phenotype demonstrate that molecular subtypes can predict the response to treatment with tyrosine kinase inhibitors and are related with prognosis. Different strategies will be recommended according to different molecular subtypes of GIST in the future for treatment optimization and individualization.