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Background: Soil salt stress is a problem in the world, which turns into one of the main limiting factors hindering maize production. Salinity significantly affects root physiological processes in maize plants. There are few studies, however, that analyses the response of maize to salt stress in terms of the development of root anatomy and respiration. Results: We found that the leaf relative water content, photosynthetic characteristics, and catalase activity exhibited a significantly decrease of salt stress treatments. However, salt stress treatments caused the superoxide dismutase activity, peroxidase activity, malondialdehyde content, Na+ uptake and translocation rate to be higher than that of control treatments. The detrimental effect of salt stress on YY7 variety was more pronounced than that of JNY658. Under salt stress, the number of root cortical aerenchyma in salt-tolerant JNY658 plants was significantly higher than that of control, as well as a larger cortical cell size and a lower root cortical cell file number, all of which help to maintain higher biomass. The total respiration rate of two varieties exposed to salt stress was lower than that of control treatment, while the alternate oxidative respiration rate was higher, and the root response of JNY658 plants was significant. Under salt stress, the roots net Na+ and K+ efflux rates of two varieties were higher than those of the control treatment, where the strength of net Na+ efflux rate from the roots of JNY658 plants and the net K+ efflux rate from roots of YY7 plants was remarkable. The increase in efflux rates reduced the Na+ toxicity of the root and helped to maintain its ion balance. Conclusion: These results demonstrated that salt-tolerant maize varieties incur a relatively low metabolic cost required to establish a higher root cortical aerenchyma, larger cortical cell size and lower root cortical cell file number, significantly reduced the total respiration rate, and that it also increased the alternate oxidative respiration rate, thereby counteracting the detrimental effect of oxidative damage on root respiration of root growth. In addition, Na+ uptake on the root surface decreased, the translocation of Na+ to the rest of the plant was constrained and the level of Na+ accumulation in leaves significantly reduced under salt stress, thus preempting salt-stress induced impediments to the formation of shoot biomass. [ABSTRACT FROM AUTHOR]