Root-affix and syllable segmentation of Uighur word bring great facilities in Uighur natural language processing. Affix in Uighur are various , they link between themselves and to a root in different ways. But there are intricate rules in their linkage. In this paper , we propose methods of handling with the basic phonetic features of Uighur words , such as the final vowel change , rules of vowel and consonant harmony , and syllable segmentation. We also summarized the word structures and phonetic structures of Uighur , and proposed some rules of Uighur word segmentation and implementation of this segmentation. According to the implementation of these rules on regular words from scientific publishing in Xinjiang , the accuracy is 95%.