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The AC-based capacitance measuring circuits are widely used in electrical capacitance tomography. In the circuit, the desired exciting and measuring signals are alternative current (AC) ones that should have a zero direct current (DC) component. However, because of the non-deal characteristics of the operational amplifiers and other electronic components, DC biases, i.e., nonzero DC components always exist in actual AC signals. The DC biases have negative influences on capacitance measurement. In the paper, theoretical analysis was carried out and a method of compensating the effect of the DC bias was introduced. A digital AC-based capacitance measuring system was constructed to implement the compensation method. Experimental results show that the signal-to-noise ratio of the system is improved by employing the proposed method.