A novel multi-microchannel biochip fiber-optic particle plasmon resonance (FOPPR) sensor system for the simultaneous detection of multiple samples. The system integrates a novel photoelectric system, a lock-in module, and an all-in-one platform incorporating optical design and mechanical design together to improve system stability and the sensitivity of the FOPPR sensor. The multi-microchannel FOPPR biochip has been developed by constructing a multi-microchannel flow-cell composed of plastic material to monitor and analyze five samples simultaneously. The sensor system requires only 30 μL of sample for detection in each microchannel. Moreover, the total size of the multi-microchannel FOPPR sensor chip is merely 40 mm × 30 mm × 4 mm; thus, it is very compact and cost-effective. The analysis was based on calibration curves obtained from real-time sensor response data after injection of sucrose solution, streptavidin and anti-dinitrophenyl (anti-DNP) antibody of known concentrations over the chips. The results show that the multi-microchannel FOPPR sensor system not only has good reproducibility (coefficient of variation (CV) < 10%), but also excellent refractive index resolution (6.23 ± 0.10 × 10⁻⁶ refractive index unit (RIU)). The detection limits are 2.92 ± 0.28 × 10⁻⁸ g/mL (0.53 ± 0.01 nM) and 7.48 ± 0.40 × 10⁻⁸ g/mL (0.34 ± 0.002 nM) for streptavidin and anti-DNP antibody, respectively.