Abstract: Objective To ev aluate the application value of oxford nanopore technology ( ONT) in the diagnosis of complex structural variations (SVs). Methods The peripheral blood sample of a patient with non-obstuctive azoospermia and complex structural vaniations was collected, and identified by the chromosome G-banding karyotype analysis and chromosomal micraray analysis ( CMA)，which were taken as the reference methods. Meanwhile, the sample was detected by the ONT to discover the cause of disease, and the detection ability of ONT for variations was evaluated. Results A total of 9 copy number variations of uncertain signifcance ( VOUS)，ineluding 4 deletions and 5 duplications, 3 regions of homozygosity ( ROH) and 15q15.3 ( containing PPIP5KI, CKMTIB, STRC and CATSPER2 genes ) deletion were identifed by the CMA. A total of 12 053 structural variations, including 6 260 deletions, 5 624 insertions, 115 duplications , 22 inversions and 32 translocations, were identified by the ONT, which could annotate 5 559 structural variations and affect 2 406 genes. The balanced translocation of 46,XY,t(1;3)( q22;q28) detected by the ONT was basically consistent with the result of karyotype analysis [ 46, XY,t(1;3) (q22;q28)]. In addition, a 3 198 bp deletion in the Chrl: 156359988-156363186 region was detected ，which could affect TSACC, RHBG and FGF12 genes. Conclusion The ONT can apidly，efficiently and accurately detect the complex structural variations of chromosomes and afected genes in human peripheral blood samples, and deletions that cannot be detected by traditional detection methods , which is a supplement to traditional methods and has important clinical application value.