The invention relates to the technical field of preparation of hydrophilic drug microspheres, in particular discloses a method for preparing a hydrophilic drug microsphere through a spray drying process. The method comprises preparation steps of: uniformly dispersing hydrophilic drug powder into an isolation oil phase to form an S/O1 type suspension, and then slowly adding into a spray solution (O2) which contains a macromolecular carrier, an anti-sticking agent and a plasticizing agent, homogeneously emulsifying to form an S/O1/O2 type spray emulsion, decompressing and drying at 60 DEG C or less through a spray drying technology after collecting the microspheres in a cyclone separator, and screening with a sieve of 80 meshes so as to prepare the hydrophilic drug twice-embedded sustained-release microsphere. The microsphere prepared by spray drying have the advantages of round shape, smooth surface, good mobility, uniform grain size distribution, high encapsulating rate, capability ofeffectively controlling burst release, and accordance with the characteristics of a long-acting preparation; and the method has the advantages of reducing consumption of a great quantity of oil substances and volatile organic solvents , greatly shortening drying time and being remarkable in effect, and is applicable to industrial production.