A method was proposed to manipulate nanoparticles through a thermal gradient. The motion of a fullerene molecule enclosed inside a (10, 10) carbon nanotube with a thermal gradient was studied by molecular dynamics simulations. We created a one-dimensional potential valley by imposing a symmetrical thermal gradient inside the nanotube. When the temperature gradient was large enough, the fullerene sank into the valley and became trapped. The escaping velocities of the fullerene were evaluated based on the relationship between thermal gradient and thermophoretic force. We then introduced a new way to manipulate the position of nanoparticles by translating the position of thermostats with desirable thermal gradients. Compared to nanomanipulation using a scanning tunneling microscope or an atomic force microscope, our method for nanomanipulation has a great advantage by not requiring a direct contact between the probe and the object.