The invention discloses a process for preparing a polynuclear ferric hydroxide-saccharide complex, including: adding an aqueous solution of an alkaline substance drop-wise into an aqueous solution of iron salt at a temperature of 5-20° C. until pH 6-8, collecting the polynuclear ferric hydroxide from the reaction mixture by a conventional method; reacting the polynuclear ferric hydroxide with a saccharide in a solution of an alkaline substance for 10-40 hours at 106-125° C. under pH 10-12, resulting in a crude product having an isoelectric point of 4.4-5.3 and a weight average molecular weight of 20,000-100,000 Daltons, and then harvesting the polynuclear ferric hydroxide-saccharide complex from the crude product. The process can precisely control the molecular weight of the polynuclear ferric hydroxide-saccharide complex without an effect on the other characteristics of the product, for example its saccharide content or isoelectric point etc. Furthermore, it is very simple and readily applicable in industry.