The invention relates to a technological method for producing a composite probiotic two-layer microcapsule by virtue of a double-emulsification method-spray drying which is suitable for various activeprobiotic composite micro-ecological preparations, which belongs to the technical field of food microorganisms. The two-layer microcapsule prepared by adopting the double-emulsificaiton-spray dryingmethod is high in probiotic embedding efficiency, good variable bacteria stability, complete in surface and is in an approximate spherical shape; and moreover, the embedded component is released afterpassing by two interfaces, so that the burst release phenomenon can be overcome, the release time can be prolonged, and the controlled-release performance is good. The production device is simple, the operation is convenient, the labor protection is facilitated, the process period is short, the productivity is high, the finished product has good acid tolerance and cholate resisting capability, the source of raw materials is wide, the price is low, the industrialized continuous mass production can be realized, and a foundation can be laid for the industrialized production of the probiotic products.