The invention relates to a method for preparing clindamycin phosphate powder filling agent, including: adding and dissolve clindamycin phosphate in alcohol solution; adding in activated charcoal to make decolorization, then roughly filtering, finely filtering, and placing to crystallize, filtering to eliminate supernatant and obtaining clindamycin phosphate crystal; then making transfer-solution for the second time, recrystallizing once, filtering and obtaining the recrystallized clindamycin phosphate crystal; drying and crushing, making split charging, capping and packaging in aseptic condition and making it. In the preparing course, it needs no high temperature treatment, need not add in additive, and its powder has good fluidity, high purity, few impurities, high bio-capability and good stability. It has no anaphylaxis and hemolysis and has no stimulation to blood vessels by intravenous injection. It adds a new clinic form of clindamycin phosphate, meeting clinic requirement.