Well-defined and controllable one-dimensional (1D) nanostructures of fullerene derivative have been prepared by an electrophoretic template synthesis method. The clusters of fullerene derivative formed in mixed solvents are introduced into the channels of porous alumina templates through a dc electric field. Four types of 1D nanostructures (solid nanowires, solid-wall nanotubes, porous nanowires and porous-wall nanotubes) have been obtained by changing the deposition parameters. This approach opens a new avenue to assemble fullerene derivatives, endohedral fullerenes, as well as other functional organic compounds, which can form clusters in 1D nanostructure arrays for applications in chemical sensors, light energy conversion devices and nanoscale electronic and optoelectronic devices.