Fe, Ni doped Ge-Sb-Se thin films are grown by electron-beam evaporation with targets sintered at low temperature, and show p-typed in conducting status. Investigated by AFM,UV-VIS,Hall and Impedance Analyzer, we observed that thin films have a more perfect network and less defects if the doped ion has a higher activity and smaller electronegative difference with the system elements, or the films are annealed. Fe and Ni doped in Ge-Sb-Se system not only take part in binding and affect the network perfection but also introduced defects near Fermi energy. Thin films doped with Ni have a more perfect network, lower neutron-hanging binding concentration and less polarons produced under AC electric field compared with Fe doped thin films, thus have smaller roughness, larger optical band gap, higher carrier mobility, lower carrier concentration and smaller dielectric loss.