A disposable capillary electrophoresis detecting device includes a fixing device, a capillary electrophoresis microchip, and an electrochemical sensor microchip. The fixing device includes two chip-fixing bases having a first chip-holding cavity horizontally arranged and a second chip-holding cavity vertically arranged. The second chip-holding cavity is substantially perpendicular to the first chip-holding cavity and faces an end portion thereof. The capillary electrophoresis microchip is horizontally placed in the first chip-holding cavity. The electrochemical sensor microchip is vertically placed in the second chip-holding cavity. In the electrochemical sensor microchip, a patterned insulation layer is located on a detecting electrode, exposes a sensor area of the detecting electrode, and is extended to two sides of the sensor area. The outlet of the separation capillary of the capillary electrophoresis microchip is aligned to the sensor area, and the distance between the outlet and the sensor area is the thickness of the patterned insulation layer.