Plant secondary metabolites have a great contribution to the agricultural and pharmaceutical industries. Their accumulation is determined by the integrated transport of target compounds and their biosynthesis-related RNA, protein, or DNA. However, it is hard to track the movement of these biomolecules in vivo. Grafting may be an ideal method to solve this problem. The differences of genetic and metabolic backgrounds in rootstock and scion make it feasible to determine the movement of target compounds, RNAs, proteins, and DNA coupled with multiple omics approaches and other molecular tools. In this review, we will introduce how to use the grafting technique, together with molecular biological tools, to reveal the differential accumulation mechanism of plant secondary metabolites from different levels. A detailed case on the transport of one diterpene alkaloid, fuziline, will be further illustrated to clarify how to reveal the specific accumulation model is shaped with the help of grafting and multiple molecular biological tools.