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This paper presents an approach to detect the presence of Dynabeads with a system based on a micro fluxgate sensor fabricated by micro-electro-mechanical systems technology. Due to the excellent performance of the micro fluxgate sensor, the detection system exhibited many advantages, such as lower minimum detectable limit, small weight, and low power consumption. Experimental results show that, applied an external magnetic field in a range of 430 μT to 600 μT, Dynabeads with a concentration as low as 0.1 μg/ml can be detected by this system. Moreover, the detection system could give an approximate quantitation to the magnetic beads.