Origami has shown the potential to design unique mechanical properties and complex three-dimensional shapes by folding through designed crease patterns on flat materials. The authors investigated a new honeycomb-based origami metamaterial called “kirigami honeycomb.” Resembling origami, kirigami honeycomb allows a single flat sheet of material with periodic slits to be folded into a honeycomb shape. Previous studies have reported successful use of this method to create various honeycomb shapes, changing only the folding line diagrams (FLDs). These previous studies have, however, considered only one-directional cross-sectional modifications; the core thickness and curvature changed only in the W-direction. This study proposes a new method that will support complex 3D honeycomb designs made from single flat sheets. A newly defined crease pattern conversion method provides arbitrary scaling of the honeycomb shape in the L-direction. The combined FLD and pattern conversion design methods encourage the cost-effective manufacture of 3D shaped honeycombs from single flat paper sheets. The proposed method is implemented to the design software, enabling to design arbitrary cross-sectional honeycomb cores with optional L-directional scaling.