Plant protein–protein interaction (PPI) networks provide valuable information for the understanding of plant biological processes. In this study, we summarized and constructed the nuclear-protein interactome of Arabidopsis based on PPIs, and preliminarily analyzed the relationships among the main pathways involving these protein interactions. These proteins are involved mainly in the plant hormone signal transduction and plant-pathogen interaction, and these pathways are linked closely by co-pathway and nodal proteins. The key nodal proteins play important roles in communication among hormonal pathways. Further analysis revealed that all of these key nodal proteins were localized in multiple organelles. High-frequency protein multi-localization analysis suggested that the multi-location proteins may play key roles in organelle communication and plant growth. Thus, the screening and study of multi-location proteins may be an important research direction. Our findings can inform new research based on protein interactions and provide novel directions for plant proteome research.