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A current-sensing atomic force microscopy was set up to measure the nanoscale capacitance spectroscopy of the two-dimensional electron gas (2DEG) of AlGaN/GaN heterostructures. The variation in the contact radius of the probe, which is important for the quantitative characterization of 2DEG, was experimentally determined by monitoring the resistive variation of the probe-sample contact and theoretically studied by numerical calculation. The current-sensing method is able to detect the change in Schottky barriers of the probe-sample contact, which affects the measurement of the threshold voltage of 2DEG. By fitting the nanoscale capacitance spectroscopy with numerical calculations, the concentration of 2DEG was quantitatively characterized. The result was comparable with that of macroscopic measurements.