The invention discloses a probe and a gene chip for thalassemia detection, a preparation method and applications. The preparation method of the probe for the thalassemia detection includes the following steps: constructing a capture interval library based on different thalassemia genes, modified genes and mutations; and designing a capture probe according to the capture interval library, wherein the capture interval library includes all globin genes and important regulatory region full-length fragments of an alpha gene cluster and a beta gene cluster, recorded breakpoint mutation sites, SNP sites selected from deletion mutations, and SNP sites on thalassemia modified genes. The preparation method of the invention is to design the probe aiming at all gene clusters and related genes of thalassemia, and so the probe can cover all thalassemia gene mutations. The preparation method is combined with Tn5 library construction and high-throughput sequencing, and so all the mutations can be covered, and the method has the advantages of simple operation, high throughput and low cost, and is suitable for large-scale population diagnosis and screening of thalassemia and research and predictionof new unknown gene mutations.