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Cucumber is a major vegetable crop grown in facilities, and its seedlings are sensitive to salinity. Thus, it is important for cucumber cultivation to research the effects of Ca(NO3)2. In this study, we investigated salt-sensitive Chunqiu (CQ) and salt-tolerant BoMei 49 (BM) seedlings, the changes to the enzymes involved in the mitochondria antioxidant system in the seedlings, and the changes in the MPTP (Mitochondrial Permeability Transition Pore) opening, mitochondrial membrane fluidity, mitochondrial membrane potential depolarization, mitochondrial electron transfer chain, and NO metabolism in response to Ca(NO3)2. Ca(NO3)2 stresses inhibited the growth of the cucumber seedlings, which showed a reduced root length, a decreased surface area and a decreased number of root tips, but a significantly increased root diameter. The mitochondrial malondialdehyde (MDA) content, H2O2 content, and O2&minus, producing rate of the two cucumber roots were gradually increased in the Ca(NO3)2 treatment. The activity of superoxide dismutase (SOD) and peroxidation enzyme (POD) gradually increased, and catalase (CAT) activity gradually decreased. The electron transport chain activity of &ldquo, BM&rdquo, was higher than &ldquo, CQ&rdquo, under Ca(NO3)2 stress. Ca(NO3)2 stress destroyed the membrane structure of the mitochondria, so that the mitochondrial body tended to bend, causing double-membrane digestion and a hollow interior. Under the stress of Ca(NO3)2, the NO3- content of the seedlings increased significantly. The contents of NH4+ and NO, as well as the activities of nitrate reductase (NR), nitrite reductase (NIR), and nitric oxide synthase (NOS) decreased significantly. These findings provide physiological insights into root damage in response to salt stress for salt tolerance in cucumber.