The Waitoushan iron deposit is a typical deposit of banded iron formations (BIFs) in the Anshan Benxi area because of its large scale and widely distributed orebodies. We carried out a comparison research over the geochemical characteristics of iron poor and iron rich ores. The results reveal that both similarities and differences exist in two iron ores. The similarities of two ores show the the ores predominantly consist of TFe2O3 and SiO2, with minor other oxidates. Combined with the characteristics of trace and rare elements, it is suggested that the iron ores of the Waitoushan iron deposit belong to Algoma BIFs, but influenced by volcanic hydrothermal activity. But the total REE concentrations of iron ores is very low, but the PAAS normalized REE and Y diagram display depletion of LREE relative to HREE, distinct Eu positive anomalies and high Y/Ho ratios, and higher concentrations of ferromagnesian trace elements relatively, such as Cr, Co and Ni. Trace and REE elements analysis suggests that ore forming material may originate from deep sea hydrothermal fluid with seawater signatures. The differences of two ores show that Fe rich ores present distinct hydrothermal signatures, with K2O more than Na2O. In addition, trace elements composition is similar to granitization granite. Combined with field investigation, it can be inferred that the higher grade iron ore may be formed by leaner iron ore though activities of migmatization hydrothermal.