The invention relates to a preparation method and application of a compound leavening agent. The preparation method comprises the steps of: separating lactobacillus plantarum, lactobacillus bulgaricus, streptococcus thermophilus, saccharomyces cerevisiae, candida rugosa, candida tropicalis and fermented pichia pastoris, as a leavening agent, from naturally fermented panada to produce a strain so as to prepare freeze-dried strain powder; weighing 1-2 parts of lactobacillus plantarum, 1-2 parts of lactobacillus bulgaricus, 1-2 parts of streptococcus thermophilus, 3-5 parts of saccharomyces cerevisiae, 3-5 parts of candida rugosa, 3-5 parts of candida tropicalis and 3-5 parts of fermented pichia pastoris based on parts by weight, and uniformly mixing to obtain the compound leavening agent. When the compound leavening agent is applied to the cooked wheaten food, bacterial contamination can be effectively prevented, the sanitation of the cooked wheaten food is guaranteed, the quality of the cooked wheaten food is improved, the production cycle is shortened, a production process is controllable, and the preparation method of the compound leavening agent lays a foundation for industrial production.