Manganese dioxide (MnO2) nanosheets are emerging for biomedical applications with excellent physical and chemical properties. Adsorption of DNA on MnO2 is important for biosensing, bioimaging, and therapy. Nevertheless, current fundamental understanding about the interaction is preliminary. Herein, UV-vis absorption spectra are applied to systematically explore the biointerfacial interaction between DNA and MnO2 with the factors of salt concentration, pH value, temperature, DNA concentration, and length. The results offer important fundamental insights into the investigation of DNA-MnO2 nanocomposites. Meanwhile, the optimal parameters are applied to construct a screen-printed electrode (SPE) modified with polymerase chain reaction (PCR) primer-decorated MnO2 nanosheets. An electrochemical PCR system is then developed for ultrasensitive detection of circulating tumor DNA (ctDNA). The limit of detection is determined to be 0.1 fM, and high selectivity is demonstrated. Combining the merits of SPE, DNA-MnO2 nanosheets, and an amplified reaction, this developed strategy shows great promise in bioanalysis, clinical disease diagnosis, and biomedicine applications.