Neuraminidase (NA), a highly sensitive recognition element for anti-influenza activity, was immobilized on a glassy carbon electrode modified with nitrogen-doped graphene-functionalized multi-walled carbon nanotube composites (N-Gr/MWCNTs) and polypyrrole (Ppy) via re-polymerization. A highly sensitive electrochemical biosensor was thus developed for the rapid screening of antiviral components in natural products, utilizing the high specific surface area and conductivity of N-Gr/MWCNTs and polypyrrole, along with the high-throughput and specific recognition capabilities of NA. Under optimized conditions, the sensor was used to assess five distinct classes of compounds, demonstrating an activity sequence of Baicalein > Baicalin > Rutin ≈ Matrine > Levistilide A, which aligns with previous literature. This study presents a convenient and efficient method for screening antiviral components in natural products, providing new strategies and technological support for the development of cost-effective, eco-friendly, and rapid screening platforms.