The interaction between DNA and mesopores is one of the basic concerns when mesoporous silica nanoparticle (MSN) is used as a DNA carrier. In this work, we have synthesized a type of mesoporous silica nanoparticle that has a Fe(3)O(4) inner core and mesoporous silica shell. This magnetic mesoporous silica nanoparticle (denoted as M-MSN) offers us a convenient platform to manipulate the DNA adsorption and desorption processes as it can be easily separated from solution by applying a magnetic field. The DNA adsorption behavior is studied as a function of time in chaotropic salt solution. The maximum amount of adsorbed DNA is determined as high as 121.6 mg/g. We have also developed a method to separate the DNA adsorbed onto the external surface and into the mesopores by simply changing temperature windows. The desorption results suggest that, within the whole adsorbed DNA molecules, about 89.5% has been taken up by M-MSN mesopores. Through the dynamic light scattering experiment, we have found that the hydrodynamic size for M-MSN with DNA in its mesopores is higher than the naked M-MSN. Finally, the preliminary result of the adsorption mechanism study suggests that the DNA adsorption into mesopores may generate more intermolecular hydrogen bonds than those formed on the external surface.