Cadmium (Cd) pollution has caused severe environmental hazards and human health risks. Phytoremediation, a green and sustainable approach, has emerged as a promising solution for Cd-contaminated soil remediation. Sedum plumbizincicola, a typical Cd hyperaccumulator, can efficiently uptake Cd from soil and translocate it to above-ground tissues, making it an ideal model for studying Cd tolerance mechanisms. Our preliminary studies demonstrated that the Rubber elongation factor (SpREFl) enhances Cd tolerance in S. plumbizincicola, and yeast one-hybrid screening identified SpNAC089 (NCBI accession number: PV553670.1) as a potential upstream transcription factor of SpREFl. In this study, we systematically investigated the regulatory mechanism of the SpNAC089 transcription factor on SpREFl. Subcellular localization assays showed that SpNAC089 is exclusively localized in the cell nucleus, and yeast transcriptional activation experiments confirmed its intrinsic transcriptional autoactivation activity. Transgenic S. alfredii overexpressing SpNAC089 exhibited significantly enhanced cadmium tolerance—with milder leaf yellowing and growth inhibition under Cd stress—and reduced Cd accumulation in roots, stems, and leaves compared to wild-type (WT) plants. Further mechanistic analyses revealed that SpNAC089 directly binds to the 1901–1950 bp region of the SpREFl promoter, which contains cis-acting elements (MBS and TCA motifs). This binding activates SpREFl transcription, thereby upregulating the activities of antioxidant enzymes (superoxide dismutase, SOD; peroxidase, POD) and reducing malondialdehyde (MDA) content under Cd stress, ultimately mitigating oxidative damage. These findings uncover a novel transcriptional regulatory pathway (SpNAC089-SpREFl) underlying Cd tolerance in S. plumbizincicola and highlight SpNAC089 as a candidate gene for optimizing phytoremediation strategies of Cd-polluted soils.