AbstractHexagonally arrayed structures of colloidal crystals with uniform surface are a good candidate for master molds to be used in soft lithography. Here, the fabrication of periodically arrayed nanostructures using poly(dimethylsiloxane) (PDMS) molds based on three‐dimensionally (3D) ordered colloidal crystals is reported. A robust, high‐quality 3D colloidal‐crystal master molds is prepared using the colloidal suspension containing a water‐soluble polymer. The surface patterns of the 3D colloidal crystals can then be transferred onto a polymer film via soft lithography, by means of the replication of the surface pattern with PDMS. Various hexagonally arrayed nanostructure patterns can be fabricated, including close‐packed and non‐close‐packed 2D arrays and honeycomb structures by the structural modification of the 3D colloidal‐crystal templates. The replicated hexagonally arrayed structures can also be used as templates for producing colloidal crystals with 2D superlattices.