The invention relates to a multifunctional composite probiotic preparation as well as a preparation method and the application thereof. The multifunctional composite probiotic preparation is prepared from lactobacillus plantarum MiuCul-01, lactobacillus acidophilus MiuLac-01, lactobacillus casei MiaoTech-01, lactobacillus rhamnosus MiaoTech-11, streptococcus thermophilus MiaoPro-01, bifidobacterium bifidum Miuyo-01, bifidobacterium lactis Miuyo-11, bifidobacterium infantis Miuyo-21 and bifidobacterium breve Miuyo-31, and the multifunctional composite probiotic preparation is prepared from lactobacillus plantarum MiuCul-01, lactobacillus acidophilus MiuLac-01, lactobacillus casei MiaoTech-01, lactobacillus rhamnosus MiaoTech-11, streptococcus thermophilus The composite probiotic preparation is prepared by a new process combining mixed bacteria inoculation, anaerobic liquid culture, solid-liquid separation, solid culture and the like, and the produced composite probiotic preparation is large in thallus quantity and high in activity, and contains metabolites generated by probiotics; the traditional Chinese medicine composition has better effects of resisting helicobacter pylori, reducing blood sugar, coordinating intestines and stomach, enhancing immunity, resisting allergy, reducing fat, losing weight and the like in human gastrointestinal tracts.