SARS-CoV-2, the pathogen of COVID-19, has introduced massive confirmed cases and millions of deaths worldwide, which poses a serious public health threat. For the early diagnosis of COVID-19, we have constructed an electrochemical biosensor-combined magnetic separation system with copper nanoflower-triggered cascade signal amplification strategy. In the proposed system, magnetic beads were utilized to fabricate the recognition element for capturing the conserved sequence of SARS-CoV-2. As the copper ions source, oligonucleotides modified copper nanoflowers with special layered structure provide numerous catalysts for click chemistry reaction. When target sequence RdRP_SARSr-P2 appears, copper nanoflowers will be bound with magnetic beads, thus prompting the Cu(I)-catalyzed azide–alkyne cycloaddition reaction through the connection of the SARS-CoV-2 conserved sequence. Then, a large number of signal molecules FMMA can be grafted onto the modified electrode surface by electrochemically mediated atom-transfer radical polymerization to amplify the signal for the quantitative analysis of SARS-CoV-2. Under optimal conditions, a linear range from 0.1 to 10³ nM with a detection limit of 33.83 pM is obtained. It provides a powerful tool for the diagnosis of COVID-19, which further benefits the early monitoring of other explosive infectious diseases effectively, thus guaranteeing public health safety.