Long non-coding RNAs (lncRNAs) are abundantly expressed in the testis, but their roles in male fertility remain largely uncharacterized. Here, we generated Jpx knockout (KO) mice and found that Jpx deficiency did not affect spermatogonial proliferation or meiosis, but predominantly impaired the post-meiotic phase of spermiogenesis. KO males exhibited reduced testis size, prolonged reproductive cycles, smaller litters, decreased sperm count, and impaired progressive motility. Their spermatozoa also showed compromised in vitro fertilization (IVF) efficiency and lower blastocyst formation rates. Ultrastructurally, KO spermatozoa had elevated teratozoospermia manifested as excessive residual cytoplasm with dispersed mitochondria and autophagic vacuoles, as well as severe midpiece mitochondrial disorganization, including disrupted sheath assembly, cristae loss, and vacuolization. Metabolomics revealed a profound defect in spermatozoal mitochondrial energy metabolism, with significant reductions in multiple glycolytic and TCA cycle intermediates (e.g., G6P and isocitrate) as well as key energy molecules (ATP, GTP, and NAD+). Mechanistically, the predominantly cytoplasmic Jpx directly bound the elongation factor EEF1A1 to form a ribonucleoprotein complex, which specifically attached to the 3' untranslated region (3'UTR) of Cul4b mRNA, thereby stabilizing the transcript and enhancing its translation. Consequently, Jpx ablation led to a substantial reduction in Cul4b, defective mitophagy (as evidenced by decreased PINK1 and LC3-II/I ratio and increased p62), mitochondrial dysfunction, and elevated oxidative stress in spermatogenic cells. Together, our findings identify Jpx as an essential post-transcriptional regulator that control mitophagy via the EEF1A1-dependent stabilization and translational promotion of Cul4b, thereby ensuring mitochondrial homeostasis, metabolic competence, and functional spermatozoon maturation.