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Background: The ubiquitin ligase HECT, UBA, and WWE domain‐containing E3 ubiquitin protein ligase 1 is essential for the establishment and maintenance of spermatogonia. However, the role of HECT, UBA, and WWE domain‐containing E3 ubiquitin protein ligase 1 in regulating germ cell differentiation remains unclear, and clinical evidence linking HECT, UBA, and WWE domain‐containing E3 ubiquitin protein ligase 1 to male infertility pathogenesis is lacking. Objective: This study aims to investigate the role of HUWE1 in germ cell differentiation and the mechanism by which a HUWE1 single nucleotide polymorphism increases male infertility risk. Materials and methods: We analyzed HUWE1 single nucleotide polymorphisms in 190 non‐obstructive azoospermia patients of Han Chinese descent. We evaluated HECT, UBA, and WWE domain‐containing E3 ubiquitin protein ligase 1 regulation by retinoic acid receptor alpha using chromatin immunoprecipitation assays, electrophoretic mobility shift assays, and siRNA‐mediated RARα knockdown. Using C18‐4 spermatogonial cells, we determined whether HECT, UBA, and WWE domain‐containing E3 ubiquitin protein ligase 1 participated in retinoic acid‐mediated retinoic acid receptor alpha signaling. We performed luciferase assays, cell counting kit‐8 assays, immunofluorescence, quantitative real‐time polymerase chain reaction, and western blotting. We quantified HUWE1 and retinoic acid receptor alpha in testicular biopsies from non‐obstructive azoospermia and obstructive azoospermia patients using quantitative real‐time polymerase chain reaction and immunofluorescence. Results: Three HUWE1 single nucleotide polymorphisms were significantly associated with spermatogenic failure in 190 non‐obstructive azoospermia patients; one (rs34492591) was in the HUWE1 promoter. Retinoic acid receptor alpha regulates HUWE1 gene expression by binding to its promoter. HECT, UBA, and WWE domain‐containing E3 ubiquitin protein ligase 1 participates in retinoic acid/retinoic acid receptor alpha signaling pathway and regulates the expression of germ cell differentiation genes STRA8 and SCP3 to inhibit cell proliferation and reduce γH2AX accumulation. Notably, significantly lower levels of HUWE1 and RARα were detected in testicular biopsy samples from non‐obstructive azoospermia patients. Conclusions: An HUWE1 promoter single nucleotide polymorphism significantly downregulates its expression in non‐obstructive azoospermia patients. Mechanistically, HECT, UBA, and WWE domain‐containing E3 ubiquitin protein ligase 1 regulates germ cell differentiation during meiotic prophase through its participation in retinoic acid/retinoic acid receptor alpha signaling and subsequent modulation of γH2AX. Taken together, these results strongly suggest that the genetic polymorphisms of HUWE1 are closely related to spermatogenesis and non‐obstructive azoospermia pathogenesis. [ABSTRACT FROM AUTHOR]