The invention discloses a rhodotorula mucilaginosa for producing opioid-like active small peptides, a screening method thereof and an application thereof. The preservation number of the rhodotorula mucilaginosa is CGMCC No. 10969. When the above bacterial strain is adopted as a livestock feed additive, the disease resistance of animals is improved, and both the morbidity and the death rate of animals are reduced. According to a separation and purification method provided in the invention, an almond is put in a mould growing environment. When a small number of moulds are produced, samples are respectively taken from the outer surface of the almond, the middle part of the almond and the interior of the almond. The above samples are mixed up and ground into powders. Water is added into the powders, and then the obtained mixture is uniformly mixed. The supernatant of the obtained mixture is taken and subjected to gradient dilution, and the obtained diluted liquid is added into a YEPD culture medium for culturing saccharomycetes. After that, the saccharomycetes is inoculated into the same medium in the streak inoculation manner to obtain single colonies. The operation is easy to conduct.