The invention discloses an orthogonal fundamental mode fluxgate sensor. The sensor includes a cobalt-based amorphous wire, an excitation current source, an induction coil, a clock source, a preamplifier, a band-pass filter, a phase-sensitive detector, a low-pass filter and a feedback channel. The cobalt-based amorphous wire, the excitation current source and the clock source constitute an excitation circuit of the sensor. The induction coil, the preamplifier, the band-pass filter, the phase-sensitive detector, the low-pass filter, the feedback channel and the clock source constitute a measurement circuit of the sensor. The excitation current source is a biased alternating current source, namely, the excitation current source contains both DC components and AC components. The DC amplitude is greater than the AC amplitude, which makes the excitation current source in a mono-polar state. Compared with the traditional bipolar current source, the biased current source can significantly suppress the Barkhausen noise of the magnetic core. Compared with the prior art, the orthogonal fundamental mode fluxgate sensor of the invention has such advantages as small size, low noise, low nonlinear error, wide frequency band and large measurement range.