The present invention relates to a capacitance sensing circuit with anti-EMI capability. A filter is coupled to a capacitor under test; receives a plurality of reference signals; and produces a first filter signal and a second filter signal. A difference circuit receives the first and second filter signals; eliminates the common-mode noise in the first and second filter signals; and produces a difference signal. The amplitude of the difference signal is related to the capacitance value of the capacitor under test. Thereby, the purpose of sensing capacitance can be achieved. In addition, by eliminating common-mode noise using the difference circuit, the anti-EMI capability can be achieved. Because the difference circuit can adjust the dynamic range of the output of the filter, the capacitance sensing circuit with anti-EMI capability can achieve capacitance sensing in few clock cycles.