The invention discloses a preparation method of a porous micro-scaffold and a composite system thereof. The porous micro-scaffold is a three-dimensional porous micro-scaffold of sodium alginate. The preparation method comprises the following steps: (1) preparation of the three-dimensional porous scaffold of sodium alginate: dissolving modified sodium alginate in deionized water, placing at 4 DEG C, placing at -20 DEG C and freeze-drying; adding a calcium chloride solution, immersing with PBS, freeze-drying again, sealing, drying and storing; and (2) preparation of the three-dimensional porousmicro-scaffold of sodium alginate: placing a three-dimensional porous scaffold of sodium alginate in a centrifuge tube, adding liquid nitrogen, and quickly breaking the scaffold by a homogenizer; adding a calcium chloride solution after the liquid nitrogen is completely evaporated, reacting, filtering, and freeze-drying particles so as to obtain the three-dimensional porous scaffold of sodium alginate. A sodium alginate composite micro-scaffold system is developed in the invention. The system can efficiently promote stem cell expansion and directed differentiation, is simple to operate and hasstrong clinical practicability.