A touch sensing system including a touch input interface and a capacitance sensing circuit is provided. The touch input interface includes a plurality of sensing capacitors for outputting a capacitance under test and a reference capacitance. The capacitance sensing circuit includes a first sensing channel, a second sensing channel, and a difference comparing unit. During a first period of the sensing period, the first sensing channel senses the capacitance under test, and the second sensing channel senses the reference capacitance. During a second period of the sensing period, the first sensing channel senses the reference capacitance, and the second sensing channel senses the capacitance under test. The difference comparing unit outputs a difference according to the capacitance under test and the reference capacitance. Additionally, a capacitance sensing method is also provided.