This study uses the historical language comparison method to study the phonetic phenomena in Early Mandarin and Uyghur literature in the Yuan and Ming dynasties. The study emphasizes the importance of classifying the nature of the material, examining the translated language and the target language, and analyzing the phonetic evolution layers. Based on this, it analyzes the Uyghur Buddhist literatures, contract literatures, inscription literatures of the Yuan Dynasty, and The Uyghur translated language literatures of the Ming Dynasty. This study finds that the literature will affect its phonetic phenomenon due to its different nature. The phonetic phenomenon reflected in Uyghur Buddhist literatures is obviously more conservative than other types of literatures of the same period, and shows more characteristics of northwestern dialects in the Tang and Five Dynasties. In contrast, the phonetic phenomenon in Uyghur contracts and inscriptions in the Yuan Dynasty is closer to the pattern of "Zhongyuan Yinyun(《中原音韻》)". In Buddhist literature, two types of phonetic transliteration can be further divided into Buddhist phonetic annotation and Chinese loanwords. There are also some differences in the phonetic performance of the two. In these literatures, the phonetic phenomenon of Buddhist phonetic annotation is the most conservative, such as the initials denasalizated, the loss of syllable codas in 宕、梗rhymes, 唐、陽rhymes that with unrounded vowels are translated into round vowels, and the entering rhyme codas are retained. The Uyghur literature in the Ming Dynasty reflected a number of Chinese phonetic phenomena, including: 1) palatalization of initial consonants; 2) retroflexion of initial consonants; 3) the labial dissimilation occurs in 山rhymes; 4) the coda -m could be mixed with -n, -ŋ; 5) The pronunciation of 坤 and 哈 are changed. This study also finds a Uyghur language sound law of "t>d/between words" in the Uyghur literature after the Yuan Dynasty; this law also affects the translation between Uyghur and Chinese.