Maturity-onset diabetes of the young (MODY) is a form of monogenic diabetes caused by single-gene mutations. MODY3, the most common subtype, results from mutations in the hepatocyte nuclear factor 1-alpha (HNF1α) gene. HNF1α is a transcription factor essential for pancreatic β-cell function and insulin production. Clinically, β-cells in MODY3 patients generally retain intact sulfonylurea receptor function, making sulfonylureas the preferred treatment. However, a novel loss-of-function variant, HNF1α-Q125ter, has been shown to induce sulfonylurea insensitivity in MODY3 patients. This study aimed to investigate the role and mechanism of HNF1α-Q125ter-mediated mitochondrial dysfunction and impaired mitophagy in new variant-induced β-cell dysfunction. Mitophagy-related protein and transcription levels were analysed by Western blotting and reverse transcription-quantitative PCR (RT-qPCR). Mitochondrial morphology was examined by transmission electron microscopy. Ins-1 cells were transfected with overexpression constructs for HNF1α-Q125ter or short hairpin RNA targeting HNF1a (shHNF1α) to assess its effects on mitochondrial function and mitophagy. Ins-1 cells expressing HNF1α-Q125ter showed decreased mitochondrial number, oxygen consumption, and energy metabolism. Correspondingly, mitochondrial morphology was damaged in an hnf1a+/- zebrafish model. HNF1α-Q125ter also inhibited mitophagy by suppressing the mRNA expression of PTEN-induced kinase 1 (PINK1), pyruvate dehydrogenase E1 subunit α1 (PDHA1), and Parkin RBR E3 ubiquitin-protein ligase (Parkin). Mechanistically, HNF1α-Q125ter impaired autophagy by downregulating phosphorylated mammalian target of rapamycin (p-mTOR) (Ser2448) and phosphorylated-70 kDa ribosomal protein S6 kinase (p-p70S6K) (Thr389). In conclusion, our findings suggest that HNF1α-Q125ter induces mitophagy dysfunction by suppressing the p-mTOR(ser2448)/p-p70S6K(Thr389) signalling pathway, providing novel insights into the mechanisms underlying sulfonylurea insensitivity in patients with this variant.