High soil sodium (Na) is a common stress in natural and agricultural systems. Roots are usually the first tissues exposed to Na stress and Na stress-related impairment of mitochondrial function is likely to be particularly important in roots. However, neither the effects of NaCl on mitochondrial function, nor its protection by several potential adaptive mechanisms, have been well studied. This study investigated the effects of NaCl stress on maize (Zea mays) mitochondrial electron transport and its relative protection by osmoprotectants (proline, betaine, and sucrose), antioxidants (ascorbate, glutathione, and α-tocopherol), antioxidant enzymes (catalase and Cu/Zn-superoxide dismutase), and mitochondrial small heat shock proteins (sHsps). We demonstrate that Complex I electron transport is protected by antioxidants and sHsps, but not osmoprotectants, whereas Complex II is protected only by low concentrations of proline and betaine. These results indicate that NaCl stress damaged Complex I via oxidative stress and suggests that sHsps may protect Complex I as antioxidants, but NaCl damaged Complex II directly. This is the first study to demonstrate that NaCl stress differentially affects Complex I and II in plants and that protection of Complex I and II during NaCl stress is achieved by different mechanisms.