To assess the effects of scion and rootstock genotypes on plant growth and the anti-oxidant defense systems of cucumber, two cucumber cultivars (“Jinchun No. 2”, a relatively salt-sensitive cultivar, and “Jinyu No. 1”, a relatively salt-tolerant cultivar) were grafted onto two rootstocks (“Figleaf Gourd”, a relatively salt-sensitive cultivar, and “Chaojiquanwang”, a relatively salt-tolerant cultivar), respectively. The grafted plants were grown hydroponically and were exposed to 0 and 100 mmol L−1 NaCl stress under greenhouse conditions. The results showed that the salt injury index, leaf Na+ content and root hydrogen peroxide (H2O2) content in the plants grafted onto Figleaf Gourd were higher, whereas the activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) in the leaves and roots were lower than those of the plants grafted onto Chaojiquanwang under NaCl stress, independent of the scion genotypes. This resulted in smaller reductions in root dry weight, shoot dry weight and leaf area in the plants grafted onto Chaojiquanwang. The salt injury index was positively correlated with the leaf Na+ content and H2O2 content in the leaves and roots, but was negatively correlated with the activities of SOD and POD in the roots. The effects of scion on the salt injury index, Na+ content in the leaves, H2O2 content and activities of POD and CAT in the roots were significant, whereas there were no significant effects of scion on the root and shoot dry weights, leaf area and leaf relative water content. Overall, these results suggest the following: (1) the salt-tolerant rootstock was more important in determining the salt tolerance of the grafted cucumber seedlings under NaCl stress compared with the scion genotypes, (2) the higher salt tolerance of the grafted cucumber seedlings could be partially attributed to the lower leaf Na+ content and root H2O2 content and higher activities of SOD, POD and CAT in the roots.