Interspecific hybrid Cucurbita rootstocks (Cucurbita maxima × Cucurbita moschata) are the most widely used rootstocks for Cucurbitaceous vegetables in the world. In recent years, scientists have focused on understanding and exploiting root architectures as new opportunities for crop improvement. Selection of parents and hybrids based on combining ability test is an effective approach in interspecific hybrid variety breeding. However, limited information is available on the combining ability tests for the rooting and graft-related traits in these rootstocks. Ondokuz Mayis University and Black Sea Agricultural Research Institute are conducting a program to breed Cucurbita rootstocks in Turkey for fifteen years. In this study, seven C. maxima (BC5F1 generation) lines as female parents and three C. moschata (S6 generation) lines as male parents were used to obtain 21 crosses. The watermelon grafted onto the interspecific hybrids and their parent rootstocks were analyzed in terms of general combining ability (GCA), specific combining ability (SCA), heritability, and heterosis for roots and graft-related traits including root volume (cm3), root length (m), root dry weight (g), hairy root rate (%), average root diameter (mm), shoot dry weight (g), graft success rate (%), and hypocotyl thickness ratio (%) by using line × tester mating design. The quotient of GCA/SCA effects for all root and hypocotyl traits were higher than 1, suggesting the preponderance of additive over non-additive gene action in the expression of these traits, whereas graft success was controlled by additive and non-additive gene effects. It was determined that average root diameter had high heritability (63.85%) and the other traits had intermediate heritability ranging from 40.59 to 58.98%. Combining ability analyses indicated that FTS5, GH12, and GRD17 lines were promising parents with greater general combining ability. Three crosses, GRD17 × FTS5, B12 × FTS5, and BH5 × CHI2 showed superior mid-parent heterosis and significant SCA for most studied characteristics. Present findings will provide significant contributions in understanding of root related characteristics and then achieving desirable improved rootstocks in C. maxima × C. moschata.