Understanding the magnetic structure of materials on a nanometre scale provides fundamental information in the development of novel applications. Here we show a site-specific electron energy-loss magnetic chiral dichroism method, first experimentally demonstrating that the use of transmitted electrons allows us to quantitatively determine atomic site-specific magnetic structure information on a nanometre scale. From one NiFe(2)O(4) nanograin in composite films, we extract its atomic site-specific magnetic circular dichroism spectra and achieve the quantitative magnetic structure information, such as site-specific total magnetic moments and orbital to spin magnetic moment ratios, by constructively selecting the specific dynamical diffraction conditions in electron energy-loss magnetic chiral dichroism experiments. The site-specific electron energy-loss magnetic chiral dichroism method shows its unique ability for solving the site-specific magnetic structure at nanoscale resolution, compared with X-ray magnetic circular dichroism and neutron diffraction. This work opens a door to meet the challenge of exploring the magnetic structures of magnetic materials at the nanoscale using transmitted electrons.