Abstract: Protein interactomics is a cutting-edge technology to identify and quantify the interaction of proteins with other metabolites or molecules like proteins, which has been an important part of plant systems biology and multi-omics research. In recent years, the rapid development of mass spectrometry-based omics technologies has facilitated great progress in methodologies for discovery and verification of the protein-metabolite interaction (PMI) and protein-protein interaction (PPI), which are the main protein interactomic technologies, showing great potential for applications in plant functional genomic and metabolomic studies gradually. Here, we present a systematic overview of the analysis strategies of different protein interactomics technologies (including PMI and PPI) in the past decade and analyze their advantages, disadvantages and specific applicable interaction types. The application progress and application strategies of protein interactomics technologies in plant research and the key technical bottlenecks that need to be overcome are also summarized. In the near future, the continuous development of interactomics technologies will further leverage the analysis of intracellular signal transduction and metabolic regulatory pathways in plants, and precise analysis of key interactions in signal networks will provide important information for the studies of the growth and development of plants and their adaptation to external environment.