The invention disclosed a sensing element integrating silicon nanowire gated-diodes with microfluidic channel, a manufacturing method and a detecting system thereof. The sensing element integrating silicon nanowire gated-diodes with a microfluidic channel includes a silicon nanowire gated-diode, a plurality of reference electrodes, a passivation layer and a microfluidic channel. The reference electrodes are formed on the silicon nanowire gated-diodes, and the passivation layer having a surface decorated with chemical materials is used for covering the silicon nanowire gated-diodes, and the microfluidic channel is connected with the passivation layer. When a detecting sample is connected or absorbed on the surface of the passivation layer, the sensing element integrating silicon nanowire gated-diodes with the microfluidic channel can detect an electrical signal change.