This invention discloses a natural mineral filter agent for desalting seawater, which is composed of attapulgite, smectite, zeolite, diatomite, mainfanite and sepiolite. The natural mineral filter agent is prepared by: pulverizing the above components, soaking, pressing, air-drying, crushing, sieving, torrefying, cooling and packaging. The contents of NaCl, KCl, Ns2SO4 and Na2CO3 in seawater are effectively decreased by ion exchange between Na+ / K+ in seawater and the natural mineral filter agent. Heavy metals such as Hg, Pb and As, chlorides and residual pesticides can be adsorbed by the natural mineral filter agent. The natural mineral filter agent can be used for late-stage purification and filtration of seawater desalting, as well as brackish water desalting in China northwestern regions.