The invention provides an autofluorescence imaging method and a system. The method comprises the following steps: acquiring the optical signals of the surface of an imaging target object at different angles; respectively modifying the optical signals acquired at different angles to obtain the optically modified data; storing the optical signal data acquired by the data acquisition unit and the data optically modified by a pre-processing unit; and carrying out the autofluorescence imaging based on the optically modified data. The method combines the current multi-angle non-contact measuring technique with the finite element imaging method and develops the posterior boundary signal modification strategy to facilitate the improvement of the imaging precision and stability of the light source. The method has important significance and application value on the development of the autofluorescence tomography.