Knockdown of NDUFA4L2 inhibited OS cell proliferation migration, and epithelial–mesenchymal transition progression, as well as promotes apoptosis in vitro. 143b, U2OS, and HOS cell lines were transfected with si-NC or si-NDUFA4L2-2 or si-NDUFA4L2-3 in hypoxic environments. (A) Protein expression of NDUA4L2, P62, LC3, Bax, Bcl-2, PARP, and GAPDH in 143b, U2OS, and HOS cells was measured using Western blotting. (B) Relative cell proliferation of 143b cells was detected by CCK-8. (C) ROS production was detected by use of a Reactive Oxygen Detection Kit. (D) Protein expression of Slug, snail, MMP2, MMP9, E-cadherin, and Vimentin was measured in 143b and HOS cells post-transfection of si-NC, si-NDUFA4L2-1, or si-NDUFA4L2-2. (E) Immunofluorescence assessments were performed to measure E-cadherin and Vimentin protein expression in 143b and HOS cells. (F) Protein expression of NDUFA4L2, E-cadherin, and Vimentin was measured in HOS cells. NX, normoxic environment; HY, hypoxic environment. nsp ≥ 0.05, *p < 0.05, ψ < 0.01, and # < 0.001 were defined as measures that indicated significant differences among treatment groups. All experiments were performed in triplicate. (F) OCR were detected in 143b and HOS cells. (G) Protein expression of NDUFA4L2, E-cadhrin, and Vimentin was measured in HOS cells.