Abstract: The present invention discloses a reconstruction method and system of fluorescence molecular tomography based on wavelet and Schur decomposition, the method including the steps of: transforming the inverse problem of fluorescence molecular tomography into a linear matrix equation; solving the linear matrix equation and updating reconstruction parameters iteratively using the obtained solution to obtain a final reconstruction result; in which, in the process of solution of the linear matrix equation, wavelet transform is performed on the linear matrix equation to obtain an overview matrix equation, Schur decomposition is performed on the overview matrix equation to obtain a subsystem with a reduced number of conditions, and the linear matrix equation is calculated using the solution of the subsystem. The present invention reduces the amount of calculation in the process of reconstruction, speedups the process of reconstruction, improves the imaging efficiency and further improves the imaging quality.