Disclosed is a method for soft soil foundation treatment through microorganism grouting sand drain. The method comprises the steps that a, a pile hole 1 is formed in a soft soil foundation to be treated, and sand is poured into the pile hole 1 to form a sand pile; b, a urease-producing microorganism solution 9 and a nutritive salt solution 10 are sequentially and evenly injected into the sand pile through a grouting tube 6, sand cementation is achieved through the microorganism induction calcium carbonate crystal technology, the concentration of the urease-producing microorganism solution 9 and the concentration of the nutritive salt solution 10 are controlled, sand in the pile body forms a specific cementation mode, and the good water permeable characteristic is ensured; c, after the microorganism grouting solidification sand pile is formed, a flexible water permeable sand cushion 4 is laid on the top of the foundation jointly formed by the sand oil and pile space soil 2, prepressing loads 5 are exerted on the top of the flexible water permeable sand cushion 4, pore water in the pile space soil 2 is made to be drained along a drainage channel formed by the sand pile and the sand cushion, the pile space soil is solidified, and the composite foundation with the high bearing capacity is formed jointly through the soft soil obtained after drainage and solidification are carried out on the microorganism grouting sand pile and the flexible water permeable sand cushion covering the soft soil.