DNA-based logic gates stimulate the development of molecular scale computers and show enormous potential in nanotechnology, biotechnology, and medicine. However, the reported detectors to date usually require one to label appropriate signal probes, resulting in not only a high cost but also potentially tedious manipulation. For the first time, we established a label-free logic gate by regarding the structure-related signal as output. Dual polarization interferometry (DPI) was employed to reveal the detailed conformational transitions occurring in the multiple-factor biomolecule interactions and then was utilized as a detection tool of logic gate. As a vital merit of this system, the dependence of the density output signal on the interaction with multiple-factor input can mimic the function of signal communication in OR, INHIBIT, and IDENTITY logic gates and the INHIBIT-OR cascade circuit. Additionally, the DPI signal with logic stringency can unambiguously distinguish conformational polymorphisms and compare structural stability. This study provides a new way for the construction of a label-free logic gate, supplements information deficiency of reaction details, and extends the application of DPI in logic operation.