Grafting has been widely used to improve quality, yield, and tolerance to biotic and abiotic stresses in plants. Tomato/potato heterografting combines two different species to create a new variety that can harvest tomato fruits and tubers from scions and rootstocks, respectively. This could be an optimal agricultural technique for improving yield and utilizing nature resources effectively, but the growth and development of rootstocks and scions after grafting are rarely described. The present study aimed to determine the effects of tomato/potato heterografting on the physiological characters, quality and yield of fruits and tubers and study the changes in photosynthetic capacity of tomato scion grafted to potato rootstock. In this study, the Zhongyan988 (ZY988) tomato cultivar four potato cultivars, Lishu6 (LS6), Qingshu9 (QS9), Hezuo88 (HZ88) and Diantongshu1 (DTS1), served as grafting parents and ungrafted tomato and potato plants were used as controls. Intergeneric grafting between tomato and potato was an effective agricultural approach that improved the yield per unit area on existing cultivated land. Under normal growth conditions, grafting had no significant effect on the photosynthetic capacity of the tomato leaves. Some characteristics related to the tomato fruit quality were improved by the potato rootstocks, including vitamin C (Vc), total soluble solids and soluble sugars; however, the titratable acidity content decreased in these grafted plants. The tomato fruit size and fruit number were affected by grafting. Grafting produced more fruit with lower average weight per fruit. Grafting had a significantly promoted tuber sprouting during the harvest period and decreased the tuber number per plant. Furthermore, the starch content and Vc level in the potato tubers were significantly decreased after grafting, but the reducing sugar content significantly increased. Scion and rootstock changes caused by grafting may be related to the accumulation and distribution of photosynthetic products and scion-rootstock interactions.