Advanced biosensors must exhibit high sensitivity, reliability, and convenience, making them suitable for detecting trace samples in biological or medical applications. Currently, biometric identification is the predominant method in clinical practice, but it is complex and time-consuming. In this study, we propose an optical metasurface utilizing the Fano resonance effect, which exhibits a sharp resonance with a transmittance of 32% at 0.65 THz. The resonance dip has a narrow bandwidth of 0.07 THz and a high Q-factor of 42. This resonance arises from the coupling of bright and dark modes, underpinned by the electromagnetic mechanism of Fano resonance. We integrated the metasurface into a microfluidic platform and fabricated low-temperature gallium arsenide photoconductive antennas (LT-GaAs-PCAs) on both sides of the microfluidics to efficiently generate and detect THz waves, significantly reducing the system's volume. The biosensor's detection limits for Escherichia coli (E. coli) and cefamandole nafate are 5 × 103 cells/mL and 5 μg/mL, respectively. Experimentally, when E. coli and cefamandole nafate solutions were sequentially injected into the microfluidic chip, a blue shift in the spectrum was observed. The sensor measured a 95.2% killing rate of E. coli by 40 μg/mL cefamandole nafate solution, with only a 3% deviation from biological experiments. Additionally, a timed killing experiment using 40 μg/mL cefamandole nafate on E. coli revealed a 93.7% killing rate within 3 min. This research presents a THz microfluidic biosensor with rapid detection, high sensitivity, and enhanced portability and integration, offering a promising approach for biomedical research, including antibiotic efficacy assessment and bacterial concentration monitoring.