Abstract Mitochondrial Ca²⁺ homeostasis is maintained through coordinated influx and efflux processes, with NCLX long recognized as the primary Ca²⁺ extruder operating via Na⁺/Ca²⁺ exchange. Here, we report cryo-EM structures of rat NCLX in cytosolic-facing occluded and open states. The central transmembrane (TM) domain of NCLX comprises ten helices arranged in two inverted, structurally similar halves, with two α-repeats forming a central ion-binding pocket.