The Y-complex, an essential peripheral component of the nuclear pore complex (NPC), plays crucial roles in nucleocytoplasmic transport, mRNA surveillance and transport, chromatin organization, and gene expression regulation. In plants, the Y-complex nucleoporins Nup96 and HOS1 are critical for modulating salt stress responses, flowering time, thermotolerance, salinity-delayed flowering, miRNA biogenesis, and hypocotyl growth. However, the regulatory mechanisms of the plant Y-complex remain largely unknown. Using proximity labeling technology, we identified several proteins labeled by Nup96 and HOS1, which will facilitate further investigation into the functions of the Y-complex in regulating these biological processes.