The invention relates to a magnetic particle manipulation apparatus for moving magnetic particles within a tubular device, wherein the tubular device includes a gel-like medium layer and a liquid layer alternately stacked within a vessel and is filled with the magnetic particles. The magnetic particle manipulation apparatus of the invention includes a vessel holding portion, a vessel pressing portion and a magnetic field applying portion. The magnetic field applying portion includes a magnetic force source. At least one of the magnetic field applying portion and the vessel holding portion includes a moving mechanism capable of moving the magnetic force source. The vessel is pressed by the vessel pressing portion. The magnetic force source is moved relatively to the vessel holding portion by the moving mechanism, so as to move the magnetic particles.