The invention discloses a fluid optical waveguide structure, which is based on the principle that the refractive index of fluid changes along with the temperature and adopts a method of electrode heating to form the fluid optical waveguide. The fluid optical waveguide comprises a substrate I, a structure layer and a substrate II, wherein the structure layer is provided with a microtube of which two ends are respectively communicated with an input port 5 and an output port 7; a pair of metal electrodes are respectively positioned at the corresponding positions of the substrate I and the substrate II, or positioned on two inner walls of the structure layer, or coat the whole microtube; the position on the substrate I corresponding to the positions of the input port 5 and the output port 7 on the structure layer are distributed with holes; and in order to ensure that the metal electrodes are insulated with the fluid, a thin polymer film can be covered on the metal electrodes. Because anyfluid at the same type can be used in the invention, the material selectivity of the fluid optical waveguide is more flexible; and by the simple control of a circuit, the invention realizes the stable light transmission in the fluid optical waveguide, thereby providing a simple and convenient tool for the optical detection of the biological cells and large biological molecules.