The Uyghur language has various inflectional affixes, complex structures and phonetic changes. The authors propose a collaborative analysis method for Uyghur morphology at character level. It includes three procedures: morpheme segmentation, morphological annotation and reduction of phonetic changes. The main characteristics of this method is to use a composite tag to represent the morpheme boundaries, annotations and phonetic changes. In addition, character sequence annotation is used to train the model. Experimental results show that the accurency of morpheme segmentation, morphological annotation and reduction of phonetic reaches 96.39%, 92.78% and 99.79% respectively. The overall accuracy of the system reaches 92.59%.