In brief Non-obstructive azoospermia (NOA) is a major cause of male infertility, with many cases having unknown origins. This study identifies two TOP6BL variants linked to NOA, revealing their impact on meiotic DNA double-strand break (DSB) formation and spermatogenesis. Abstract Azoospermia, particularly NOA, affects approximately 1% of men and accounts for 10–20% of male infertility cases, with a substantial proportion of NOA cases remaining of unknown aetiology. This study investigated the role of the TOP6BL gene in NOA in two consanguineous Han Chinese families. Two distinct variants in TOP6BL , c.1067C>G:p.Pro356Arg and c.1543C>T:p.Arg515Ter (NM_024650.3 → NP_078926.3), were identified, both linked to NOA in these families. These variants disrupted meiotic DNA DSB formation, an essential process in spermatogenesis, resulting in meiotic arrest at the zygotene stage. Functional analyses revealed that the p.Arg515Ter variant impaired binding to REC114 and disrupted interaction with SPO11, whereas the p.Pro356Arg variant did not affect protein binding but impaired self-dimerisation. Moreover, deletion of the TOP6BL central region in mice induced meiotic arrest, confirming the critical role of this region in spermatogenesis. These results highlight the diverse mechanisms by which TOP6BL variants contribute to NOA and highlight the pivotal role of the TOP6BL intermediate region. Thus, disruption of meiotic DSB formation is a key mechanism underlying male infertility.