The HAP nanoparticles were synthesized with a chemical co-precipitation method. It was monodispersed in needle shape. Its average diameter was 30 nm and length was 70 am. Human liver cancer cells and normal hepatic cells were treated by hydroxyapatite nanoparticles. SR-XRF analysis was used to detect the content variation of calcium and phosphor elements in cancer cells when the cells were treated by hydroxyapatite nanoparticles. It was introduced to reveal the anti-cancer mechanism of HAP nanoparticles. Experiments verified that the contents of calcium and phosphor elements in hepatocellular carcinoma had been obviously increased after the cells were treated by hydroxyapatite nanoparticles. And the contents increased with hydroxyapatite concentration and treatment time increasing. The Ca/P molar ratio in treated cell was different from both that in hydroxyapatite and that in untreated cancer cell. Apatite nanoparticles evidently altered the calcium and phosphor environments in treated hepatocellular carcinoma cells. That finally halted the proliferation of carcinoma cells.