The micro fluxgate sensors have shown high sensitivity for the magnetic beads detection. For portable magnetic biological detection, Co-based amorphous ribbons with high permeability and low saturation magnetic induction are chosen as core materials to lower the operation requirements of the fluxgate-based magnetic beads detection. The micro fluxgate sensors with single-layer core and bi-layer core are fabricated by Micro-Electro-Mechanical System technologies, which exhibit a power consumption of 10.88 mW and 24.48 mW, a sensitivity of 1644 V/T and 1456 V/T, and a noise of 1.66 nT/Hz1/2@1 Hz and 2.32 nT/Hz1/2@1 Hz, respectively. The Dynabeads with concentrations of 300 μg/ml in 10 μl are detected by the micro fluxgate-based sensing system based on static response, and the results show signal change ratio of 12.2% and 9.2% under the max signal difference at 215 μT and 480 μT of the bias magnetic field for two kinds of the sensors, respectively, which is near the saturation point of the sensors. The fluxgate-based bead detection system with Co-based ribbon core presents low demands for the bias magnetic field and power consumption.