Polyploid seeds production is laborious, complicated, and costly work. Tetraploid and triploid plants produce a fewer number of seeds/fruit, and triploid embryos are fairly weak, covered with a more hardened seed coat as compared to diploid seeds. Here we investigated the interactive effect of new grafting technique of polyploid watermelon scion onto rootstock on plants' survival rate, biochemical, and hormones contents. In this study, three different branches, apical meristem (AM), branch with 1 node (1N), and 2 nodes (2N) from di, Tri, and tetraploid watermelon plants, were used as scion and grafted onto squash rootstock. The results showed highly significant differences between polypoid watermelon when 1N using as a scion, tetraploid showed maximum survival rates, higher contents of hormones, and antioxidants (AOX) activities, compared to diploid, these may be the possible reasons for high compatibility in tetraploid and degrading the grafting zone in diploid. RTq-PCR results confirm that the expression of genes linked to compatibility is consistent with the hormonal and AOX activities. This study provides an alternative and economical approach to produce more tetraploid and triploid plants for breeding or seeds production by using branches as scions.