The present invention discloses a field effect transistor structure-based pH sensing device and a manufacturing method thereof. The manufacturing method is as follows: firstly, a front gate oxide layer and a gate layer are deposited on the surface of a semiconductor layer of a semiconductor substrate on an insulating layer, a gate electrode structure is formed by etching of the front gate oxide layer and the gate layer; secondly, a source-drain structure is formed by doping of the semiconductor layer of the semiconductor substrate on the insulating layer on both sides of the gate electrode structure, and the gate electrode structure and the source-drain structure together form a field-effect transistor structure; and further, photolithography is performed on the back surface of a silicon substrate on the insulating layer, a supporting substrate and a buried oxide layer are etched until the lower surface of the semiconductor layer, and a back gate oxide layer is deposited on the lower surface of the etched semiconductor layer to complete the preparation of the pH sensing device. The method utilizes the contact between a solution to be tested and a back gate of the field-effect transistor to form a double-electric-layer structure on the surface of the back gate, by changing of the Zeta potential of the double-electric-layer on the surface of the back gate in different pH solutions, the threshold voltage of the field-effect transistor can be changed, the change of the resistance of the sensing device under a fixed bias voltage can be further led, the pH value of the solution can be tested.