The invention relates to an in-vivo fluorescence molecule imaging and modeling method which can invoke a plurality of imaging algorithms and belongs to the technical field of fluorescence molecule imaging. The in-vivo fluorescence molecule imaging and modeling method is characterized in that the method is realized by controlling a florescence molecule imaging apparatus by a computer; a Microsoft main control interface program, a hardware control program package, a software library experimental data conversion and algorithm parameter alternating module, a DLL format DLL document that internally contains a C language library and a MATLAB software, and a rebuilding algorithm program library that internally contains a finite element analysis software and a kernel of the MATLAB software are arranged in the computer; in addition, an open-source image processing library is also contained. The in-vivo fluorescence molecule imaging and modeling method can automatically realize the fluorescence molecule imaging and realize the rebuilding algorithm of the density and the position of the fluorescence group and renovate the algorithm kernel conveniently.