This study investigated whether grafting cucumber (Cucumis sativus L.) onto pumpkin (Cucurbita moschata Duch.) rootstocks can induce phenotypic variations in the self-bred cucumber progeny. The phenotypic traits of the self-pollinated progeny of grafted ‘Zhenghuang 1409’ cucumber were significantly different from those of the naturally rooted ‘Zhenghuang 1409’ parent line. Compared with the ‘Zhenghuang 1409’ cucumber inbred line, the first self-pollinated and naturally rooted generation of grafted cucumber displayed reduced length and width of the leaf at the node of the second female flower, a tapered petiole and stem, increased internode length, shorter plants, decreased fruit diameter, longer fruit stalk, thicker pulp, decreased seed length and width, and a lower 100-grain weight. Similar changes in most of these phenotypic traits were observed in the second generation of self-pollinated plants from grafted cucumber. By observing plant phenotypic traits, two leaf phenotypic variations were observed in the first generation of selfed grafted cucumber, and these two phenotypes were inherited in the second selfed generation.