Lithographic scaling of periodic three-dimensional patterns is critical for advancing scalable nanomanufacturing. Current state-of-the-art quadruple patterning or extreme-ultraviolet lithography produce a line pitch down to around 30 nm, which might be further scaled to sub-20 nm through complex post-fabrication processes. Herein, we report the use of three-dimensional (3D) DNA nanostructures to scale the line pitch down to 16.2 nm, around 50% smaller than state-of-the-art results. We use a DNA modular epitaxy approach to fabricate 3D DNA masks with prescribed structural parameters (geometry, pitch and critical dimensions) along a designer assembly pathway. Single-run reactive ion etching then transfers the DNA patterns to a Si substrate at a lateral critical dimension of 7 nm and a vertical critical dimension of 2 nm. The nanolithography guided by DNA modular epitaxy achieves a smaller pitch than the projected values for advanced technology nodes in field-effect transistors, and provides a potential complement to the existing lithographic tools for advanced 3D nanomanufacturing. Epitaxially grown 3D DNA masks with prescribed geometry, pitch and size improve the resolution of reactive ion etching-based nanolithography, scaling the line pitch down to 16.2 nm and the critical dimension size to 7.2 nm.