The invention discloses a fluorescent molecular tomography imaging reconstruction method based on limited projection of double grids. The method includes the following implementation steps that firstly, measurement data is acquired; secondly, the coarse grid is reconstructed, and a feasible region of a fluorescent target is provided for reconstruction of the refined grid; thirdly, the refined grid is reconstructed under the feasible region, and three-dimensional distribution of the fluorescent target is achieved. The fluorescent molecular tomography imaging reconstruction method is based on the optical transmission theory and a finite element method, optical property parameters, anatomical structures and other prior information are utilized, single-point excitation is adopted, limited angle measurement is adopted, a double-grid strategy is utilized, a reconstructing result of the coarse grid provides the feasible region of the fluorescent target for reconstruction of the refined grid, and therefore morbidity of problems is reduced, a reconstruction result of fluorescent molecular tomography imaging is effectively improved, and the method has important application value in the fields of optical tomography three-dimensional reconstruction algorithms and the like.