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Controlling the self‐assembly of DNA nanostructures using rationally designed logic gates is a major goal of dynamic DNA nanotechnology, which could facilitate the development of biomedicine, molecular computation, et al. In previous works, the regulations mostly relied on either toehold‐mediated strand displacement or stimuli‐driven conformational switch, requiring elaborately‐designed or specific DNA sequences. Herein, we reported a facile, base‐sequence‐independent strategy for logically controlling DNA self‐assembly through external molecules. The INHIBIT and XOR logic controls over the assembly/disassembly of DNA polyhedra were realized through cystamine (Cyst) and ethylenediamine (EN) respectively, which were further integrated into a half subtractor circuit thanks to the sharing of the same inputs. Our work provides a sequence‐independent strategy in logically controlling DNA self‐assembly, which may open up new possibilities for dynamic DNA nanotechnology.