The invention discloses a probe set for detecting whole exons of extended genetic diseases. The probe set for detecting the whole exons of the extended genetic diseases comprises a standard whole exonprobe set, a whole genome copy number variation probe, and a mitochondrial loop full-length probe, and the genetic diseases comprise 6161 genetic diseases; the standard whole exon probe set can detect the genetic diseases caused by whole exon mutation, the genetic diseases comprise nervous system diseases, metabolic system diseases, endocrine system diseases, digestive system diseases, skeletal system diseases, urinary system diseases, immune system diseases, cardiovascular system diseases, blood system diseases, integument system diseases, ophthalmic system diseases, ear system diseases, respiratory system diseases, and genital system diseases; and the density of the mitochondrial probe is 6X; test samples comprise blood, fresh tissue, FFPE samples, and saliva. The invention discloses using method and kit and application of the probe set for detecting the whole exons of the extended genetic diseases.