A method for preparing low-background cement includes: uniformly mixing a seed crystal of cement, C.sub.4AF whiskers, and high-magnesium raw material to yield a first mixture, calcining the first mixture at 1400-1500? C., to yield a low-background clinker, the first mixture including 1.0-5.0 wt. % of the seed crystal of cement, 1.0-5.0 wt. % of the C.sub.4AF whiskers, and the balance is the high-magnesium raw material; and grinding a second mixture of the low-background clinker and gypsum, to yield low-background cement. The seed crystal of cement is a high-magnesium and low hydration heat clinker, has a specific activity of Ra-226 radioactive nuclides within 50 Bq/kg, and the MgO content of the clinker is between 4.0 wt. % and 5.0 wt. %, with 50 wt. %?C.sub.3S?55.0 wt. %; and the high-magnesium raw material has a MgO content between 2.5 wt. % and 3.0 wt. %.