The non-structural (NS1) protein is a multifunctional molecular protein encoded by influenza A virus genome. NS1 plays an important role in inhibition of host immune responses. In order to assess the cellular localization of NS1 in different influenza A virus subtypes, we performed the immunofluorescence assay to observe the cellular location of NS1 after infection with influenza A virus WSN (H1N1), PR8 (H1N1), CA04 (H1N1), SD (H9N2) and AH01 (H7N9) in A549 cells and MDCK cells respectively. According to the results, NS1-WSN and NS1-PR8 accumulated mainly in cytoplasm at 24 h post infection, while the NS1-CA04 and NS1-SD appeared major in the nucleus. We also observed localization of NS1 by transfected 293T cells with plasmids which encoding the full-length NS1 from WSN, SD and AH01. The key sites which might determine the different cellular localization of NS1 were chosen by sequence alignment, and seven residues which were different between WSN, PR8 and CA04, SD and AH01 were finally focused. However, we found that single mutation of these residues could not alter the localization of NS1. The data indicated that the difference of location might not be caused by substitution of a single site, which contributes to our understanding of the diverse regulation of host factors during different subtypes of influenza virus infection.