In phonology, whether there are other criteria for the classification of long and short vowels besides the distinction of word meaning is the focus of research on the length of vowels from a modern phonetic point of view. This paper experiments on the long and short vowels of Mongolian from hearing and perceptual perspectives, and explores the process of perceptual decoding concerning vowel duration. The research found that: (1) Long and short vowels differ significantly in the range and boundaries at the level of auditory sense. (2) At the cognitive level, the brain’s process of assorting long and short vowels is distinct conspicuously. (3) Word meaning has a great influence on vowel type perception.