A magnetic sensing apparatus and a magnetic sensing method thereof are provided. The magnetic sensing apparatus includes a reference magnetic field (MF) generating unit, a MF sensing unit, a signal processing unit, a calibration unit and a frequency generating unit. The MF sensing unit senses an external MF and a reference MF to provide a MF sensing signal. The signal processing unit receives and transfers the MF sensing signal into an output signal. The calibration unit calibrates the output signal according to the MF sensing signal. The frequency generating unit provides an operating frequency. The reference MF generating unit provides the reference MF according to the operating frequency, and the MF sensing unit senses the external MF and the reference MF according to the operating frequency.