The invention discloses a method for preparing a human prothrombin complex from plasma. The method comprises: directly adsorbing the human prothrombin complex from the plasma by using DEAE A-50 gel, filling the adsorbed A-50 gel into a chromatographic column of a fixed bed, pumping eluant into the filled chromatographic column by using a peristaltic pump for online washing and elution, performing S/D inactivation on the eluant, and performing secondary chromatographic purification by using the chromatographic column of the fixed bed to obtain a high-purity human prothrombin complex product. According to the method, elution flow and speed can be accurately controlled by online elution after filling the gel into the column, the problems of contamination, cross contamination, gel leakage and the like caused by an open operation are reduced, an obtained product is high in purity, an IX factor titer can exceed 27IU/ml, and the IX factor specific activity exceeds 0.8IU/mg protein. Meanwhile, a self-flushing type filter with a pressure difference controller and an automatic solid matter stripping system is adopted, so the pressure difference in the whole filtering process is stable and controllable, gel particles can be well protected, broken colloidal particles flowing into a plasma tank in the filtering process are remarkably reduced, and gel losses in a production process can be reduced by above 20%.