Solid-state nanochannels (SSN) have great development potential as a biosensing interface. The integration of two-dimensional nanomaterials with nanochannels endows SSN with diverse properties, including distinguishing DNA nanostructures. In this study, by modifying MoS 2 nanosheets, the outer surface of SSN could be endowed with robust adsorption properties for single-stranded DNA. Therefore, DNA tetrahedrons connected with single-stranded DNA could remain on the SSN surface, whereas DNA tetrahedron dimers with full double-stranded structures formed by the presence of target microRNA cannot be retained on the surface of nanochannels. The change in the DNA nanostructure generated by the target recognition process could cause variations of steric hindrance and electrostatic repulsion on the surface of the SSN. The variations were reflected by the free diffusion flux of [Fe(CN) 6 ] 3− . Then, the sensitive electrochemical detection method for microRNA was established, and the detection limit of the method for microRNA-31 was as low as 0.5 fM. The study provided a promising approach for the ultrasensitive detection of biomarkers, thereby offering potential means for early diagnosis of the related diseases.