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(R)-1,3-butanediol is an important pharmaceutical intermediate, and the synthesis of (R)-1,3-butanediol using green biological methods has recently been of interest for industrial application. Here, a novel strain QC-1 that efficiently transforms 4-hydroxy-2-butanone to (R)-1,3-butanediol was isolated from soil samples. Based on morphological, physiological, and biochemical tests and 5.8S-intal transcribed spacer sequencing, the strain was identified as Pichia kudriavzevii QC-1. The reaction conditions were optimized to 35 ℃, pH 8.0, rotation speed 200 rpm, and 6:5 mass ratio of glucose to 4-hydroxy-2-butanone. Evaluation of the effects of 4-hydroxy-2-butanone concentrations on yield and cell survival rate showed that 85.60 g·L-1 product accumulated, with an enantiomeric excess of more than 99%, when 30 g·L-14-hydroxy-2-butanone was added at 0, 10, and 30 h in a 3-L bioreactor. Thus, strain QC-1 showed excellent catalytic activity and stereoselectivity for the synthesis of (R)-1,3-butanediol from 4-hydroxy-2-butanone.