Nanoparticle (NP)-carbon nanomaterial hybrid structures have garnered significant attention due to their synergistic effects. Based on their interesting properties, hybrid nanomaterial-based sensing platforms have been investigated to achieve high sensitivity and selectivity detection. In our study, binary-NP-decorated carbon nanotubes (bNP-CNTs) were successfully synthesized through a simple two-step method and applied as a biosensing platform. Gold (Au)/iron-oxide magnetic NP-decorated CNTs (Au/MNP-CNT) were used for influenza and norovirus DNA sensing channels. To demonstrate biosensing, first, the Au/MNP-CNTs were magnetically aligned on a Pt-interdigitated electrode, and then, a thiol-group-functionalized probe DNA was attached to the Au NP surface on the bNP-CNT hybrid structure through thiol chemistry. DNA hybridization between the target influenza or norovirus DNA and probe DNA was measured to monitor an electrical conductivity change of the Au/MNP-CNTs. Various concentrations of target DNA from 1pM to 10nM were monitored, and the limits of detection for influenza virus and norovirus were calculated to be approximately 8.4pM and 8.8pM, respectively. The specificity was confirmed using different mismatched DNA sequences, showing high specificity. Therefore, this Au/MNP-CNT-based DNA sensing system exhibited excellent detection potential, and such hybrid materials could be universally applied as a highly sensitive and selective biosensing system.