The transport properties of a single wall carbon tube with transition metal atoms embedded in it are studied by using the first principles method based on the density functional theory and the nonequilibrium Green’s function. Different transition metal atoms filled in the carbon tube are investigated, and the respective charge and spin transport properties are studied. The conductance of the nanotube is found to be distinctive for different metal elements encapsulated, and quantized reductions of conductance can be seen by a quantum unit (2e2/h). In particular, nanotubes with two iron atoms encapsulated in display different I-V curves when the spins of the two iron atoms are in parallel and antiparallel states respectively. These results can be explained by spin-dependent scattering and charge transfer. The encapsulation may tailor the doping and add magnetic behavior to the carbon nanotubes, which would provide a new and promising approach to detect nanoscale magnetic activity.