Trinucleotide repeat-containing gene 6A protein (TNRC6A) is an essential protein for microRNA-mediated gene silencing. TNRC6A functions in the cytoplasm as a platform protein interacting with Argonaute protein, on which microRNA is loaded for RNA silencing, and decapping enzymes or deadenylation protein complexes to induce mRNA degradation. We previously revealed that TNRC6A shuttles between the cytoplasm and nucleus. However, the function of TNRC6A in the nucleus is unclear. Here, we performed a comprehensive identification of the nuclear and cytoplasmic interacting proteins of TNRC6A protein by mass spectrometry and identified multiple proteins involved in the nuclear and cytoplasmic complexes. We found that many RNA degradation pathway proteins were involved in both nuclear and cytoplasmic TNRC6A complexes, suggesting that RNA silencing may occur via TNRC6A in both nucleus and cytoplasm or that they were involved in other important function in the nucleus. Furthermore, proteins identified in the nuclear TNRC6A complex were categorized into the spliceosomal pathway. This may mean that TNRC6A regulates splicing in the nucleus. In contrast, pathogen infection- and RNA transport-associated proteins were identified in the cytoplasmic TNRC6A complex. Thus, TNRC6A may be also involved in these pathways in the cytoplasm.