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Tomato/potato heterografting‐triggered phenotypic variations are well documented, yet the molecular mechanisms underlying grafting‐induced phenotypic processes remain unknown. To investigate the phenotypic and transcriptomic responses of grafting parents in heterografting in comparison with self‐grafting, tomato (Sl) was grafted onto potato rootstocks (St), and comparative phenotyping and transcriptome profiling were performed. Phenotypic analysis showed that Sl/St heterografting induced few phenotypic changes in the tomato scion. A total of 209 upregulated genes were identified in the tomato scion, some of which appear to be involved in starch and sucrose biosynthesis. Sl/St heterografting induced several modifications in the potato rootstocks (St‐R), stolon number, stolon length and tuber number decreased significantly, together with an increase in GA3 content of stolon and tuber, compared with self‐grafted potato (St‐WT). These results indicate that the tomato scion is less effective at producing substances or signals to induce tuberization but promotes stolon development into aerial stems and sprouting. RNA‐Seq data analysis showed that 1529 genes were upregulated and 1329 downregulated between St‐WT and St‐R; some of these genes are involved in plant hormone signal transduction, with GID1‐like gibberellin receptor (StGID1) and DELLA protein (StDELLA) being upregulated. Several genes in auxin, abscisic acid and ethylene pathways were differentially expressed as well. Various hormone signals engage in crosstalk to regulate diverse phenotypic events after grafting. This work provides abundant transcriptome profile data and lays a foundation for further research on the molecular mechanisms underlying RNA‐based interactions between rootstocks and scions after tomato/potato heterografting.