The development process of fermented milk products with low-allergenic potential usually begins with the isolation and screening of strains. However, this bottom-up screening method is time-consuming and heavy workload. Once the target strain is not screened, it will cause a waste of time and money. This experiment adopted a top-down method to screen strains quickly and efficiently and prepared a fermented milk with low whey protein allergenic potential. The traditional fermented dairy products from Xinjiang are a good source for screening functional strains. We took 59 traditional fermented dairy products from Xinjiang as samples. The antigenicity of α-lactalbumin (α-LA) and β-lactoglobulin (β-LG), the main allergenic proteins which are easy to cause human allergy, were taken as the indicators. Through direct screening of the fermented dairy product with the lowest antigenicity, the BZ-21 sample was selected as the target sample. The 13 strains isolated from the BZ-21 sample were safe, and the antigenicity and immunoglobulin E (IgE)-binding capacity of the fermented milk prepared under optimized fermentation conditions were reduced. The results showed that the top-down screening method used in this experiment was effective, and these 13 strains will be potential probiotics in the development of low-allergenic dairy products.