Through the infrared spectroscopic and electron microprobe analysis of the small-scale 6th rhythmic unit, the content of catios and anions was determined. The result shows that the content of major elements rise and fall indistinctly while F- in the apatite near the bottom of No.3 orebody was replaced by Cl-, forming chlorapatite. This seems one of the reasons for the inversely graded layers and the rhythmic structure of the layered rocks in the Fanshan igneous complex.