The invention discloses a kit for simultaneously detecting thalassemia mutant type and deletion type and application thereof, wherein the kit includes a plurality of amplimer groups for amplifying thalassemia genes; the amplimer groups include primers designed by aiming at alpha globin genes and beta globin gene, and mutant type detecting primers aiming at HBA1 genes, HBA2 genes and HBB genes, anddeletion type detection primers aiming at alpha thalassemia genes -alpha 3.7, -alpha4.2,--SEA,--THAI and beta deletion type SEA-HPFH, sinotype and Taiwantype. Through adopting the kit, the thalassemia mutant type and deletion type can be simultaneously detected, particularly, seven common deletion types and more than 300 mutant types can be simultaneously detected, and novel mutant types can be found out; furthermore, the cost is low, and the kit is much superior to the conventional thalassemia detection kit.