Abstract Soil salinization is the main ecological problem in northwestern China, the widely used rootstock 1103 P is still can not meet production requirements in severely salinized soil. The aim of this study was to explore the NaHCO3 resistance mechanism indifferent grape rootstocks, the NaHCO3 resistant strains SN15 and SN17 (hybrids of ‘Zuoshan1’ and ‘SO4’) were used as materials, and the 1103 P strain was used as a reference. The root system configurations were scanned, the flow rate of Na+ and K+were examined by Non-invasive Micro-test Technology, NMT, the Na+ and K+ content, and the relative expression of Na+ and K+ transporter genes were measured under 50 mM NaHCO3 treatment. The total root length, root surface area and average root diameter of SN15 decreased the least after 48 h of NaHCO3 treatment, and the flow rate of the Na+ and K+ efflux in the SN15 and SN17 rootstocks was significantly lower than that in 1103 P. The Na+ content in the roots and leaves of SN15 increased the least, and K+ decreased less than that of the control after NaHCO3 treatment. The relative expression of the VvHKT genein SN15 and SN17 was higher after NaHCO3 treatment. The relative expression of VvNHXP in SN15 increased and peaked at 3.81 times that of the control. Expression of VvNHXP in SN17 peaked at 3.26 times that of the control. Expression of VvNHXP in1103 P was not significantly different. The roots of SN15 and SN17 were less affected by NaHCO3 stress, had an increased ability to excrete sodium and retain potassium, and showed decreased Na+ accumulation. The VvHKT and VvNHXP genes play important roles in mitigating NaHCO3 stress.