Abstract Targeted regulation using transgrafting technology has been becoming a trend. However, the mechanisms of transgene-derived signal communication between rootstocks and scions remain unclear in woody plants. Here, we grafted wild type (WT) walnut (Juglans regia L.) on WT (WT/WT), JrGA20ox1 (encodes a gibberellin 20-oxidase) overexpressed (WT/OE) and JrGA20ox1-RNAi transformation (WT/RNAi) walnut in vitro, respectively. We aimed to elucidate the mechanisms of JrGA20ox1-derived signal communication under PEG simulated drought stress between rootstocks and scions in walnut. We demonstrated that JrGA20ox1-OE and JrGA20ox1-RNAi rootstocks could transport active GAs and JrGA20ox1-RNAi vector produced sRNAs to WT scions under PEG simulated drought stress, respectively. The movement of sRNAs further led to a decline in JrGA20ox1 expression and active GA content successively. Meanwhile, the unknown signals may mobile between rootstocks and scions. The mobile signals reduced the expression of a series of GA-responsive and GA-nonresponsive genes, and induced ROS production in guard cells and the increase of ABA content, which may be contributed to the drought tolerance of WT/RNAi, while WT/OE is in an opposite manner. The findings suggest that JrGA20ox1 derived rootstock-to-scion movement of signals are involved in drought tolerance of scions. Our research will provide a feasible approach for studying signal communication in woody plants.