Self-assembly of Keggin-type polyoxometalates (POMs) with diammonium ions containing oligo(ethylene oxide) units form parallelepiped or octahedral nanocrystals. These structures are tunable depending on the chemical structure of the ammonium ions and preparative conditions. The ether linkages in these ammonium ions exert conformational flexibility, which is essential to achieve long-range regular molecular alignments in the nanocrystals.