The invention discloses a preparation method of chitosan/sodium polyphosphate porous microcarrier, which comprises the following steps: dropping chitosan into sodium polyphosphate solution under high pressure through a high-pressure pulse microcapsule forming device to form microspheres, cross-linking the microspheres with glutaric dialdehyde, and freezing-drying, thereby forming the chitosan/sodium polyphosphate porous microcarrier of a three-dimensional structure. The chitosan/sodium polyphosphate porous microcarrier prepared in the method has the advantages of good roundness and uniform particle size distribution. In addition, due to the adoption of the freezing-drying technology under the condition that the pH of the sodium polyphosphate is ensured during the preparation of the chitosan/sodium polyphosphate porous microcarrier, the particle size of the prepared chitosan/sodium polyphosphate porous microcarrier is 15-20 mum, the porosity thereof is close to 90 percent, and the water absorbing capacity thereof is up to 8 times.