Seed germination is a critical checkpoint for plant survival under stresses, which requires functional mitochondria for energy and signal supply. Mitochondrial ALTERNATIVE OXIDASE 2 (AOX2) is specifically and highly expressed at early seed germination; however, its regulatory mechanism remains unknown. Here, the mutant (aox2), over-expression (AOX2OE) and complementation (aox2Comp, proAOX2::gAOX2/aox2) lines were used to investigate AOX2 roles. AOX2 transcript was significantly up-regulated under ABA, NaCl, H2O2, PEG6000 or mannitol treatments during seed germination. Compared with WT and aox2Comp, seed germination and greening were delayed in aox2 under NaCl treatment but enhanced in AOX2OE lines. The transcripts of key genes related to ABA biosynthesis and signal transduction were up-regulated in aox2 compared with those in WT under salt stress. Consequently, the higher ABA level was found in aox2. Na2WO4, the inhibitor of ABA biosynthesis, significantly enhanced germination rate of aox2. Mutation of ABA-INSENSITIVE 3 (ABI3) or ABI4 can partially reverse the salt-sensitive phenotypes of aox2. Yeast one-hybrid, D-luciferin enzyme (LUC) assay and transient expression experiments further revealed ABI3 and ABI4 can directly interact with AOX2 promoter and enhance its expression. Reactive oxygen species (ROS), mainly produced from the root tip mitochondria of germinated seeds, were accumulated more in aox2 than those in WT. Exogenous ascorbic acid (AsA) decreased ROS level and fully rescued the salt-hypersensitive phenotypes of aox2. Taken together, AOX2 plays an important role in Arabidopsis seed germination through regulating ABA signal and ROS homeostasis under salt stress; in the process, ABI3/ABI4 is indispensable for salinity-induced AOX2 expression.