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A 27-year-old patient with azoospermia and low intelligence was reported having a rare karyotype 47,XYY,dup(13q12.11),t(4;9)(q21.1;q22.3),r(21)(p12q22.3). Clinical genetic tests, including next-generation sequencing (NGS), karyotyping, fluorescence in situ hybridization (FISH), and azoospermia factor (AZF) microdeletions, were conducted. The results showed that (1) one copy of chromosome 21 lost a short arm and appeared as a marker, but subsequent detection confirmed that it was a ring 21; (2) there was a reciprocal translocation between chromosome 4 and chromosome 9; (3) NGS revealed a duplication of 0.3 Mb on 13q12.11 and two Y chromosomes; (4) the Y chromosome showed no AZF microdeletions; and (5) FISH confirmed the two Y chromosomes. To our knowledge, this is the first reported case with rare karyotype, combined with four abnormal chromosomal changes simultaneously. Because no Online Mendelian Inheritance in Man genes were found in duplication fragment on 13q12.11, this duplication is not associated with low intelligence.