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<b>Objective:</b> There is evidence that type 2 diabetes (T2DM) is affected by gut microbiota, and gut microbiota diversity modified by diet. To investigate its modifications in Uyghur patients with different glucose tolerance, we enrolled 561 subjects: newly diagnosed T2DM (<i>n</i> = 145), impaired glucose regulation (IGR) patients (<i>n</i> = 138) and in normal control (NC) population (<i>n</i> = 278). <b>Methods:</b> The nutrient intake in food frequency questionnaire was calculated by R language. The regions V3-V4 of 16S ribosomal RNA were sequenced by using Illumina Miseq platform. Sequences were clustered by operational taxonomy units, gut microbiota composition, and diversity was analyzed. Correlations between bacterial composition at different level and dietary factors were evaluated. <b>Results:</b> The α-diversity was highest in NC, followed by T2DM and IGR; β-diversity distinguished between patients and NC. Compared to NC, <i>Saccharibacteria</i> was significantly increased in T2DM and IGR. <i>Deferribacteres</i> was significantly increased in T2DM compared to NC and IGR. <i>Veillonella, Pasteurellaceae</i>, and <i>Haemophilus</i> were over-represented in IGR. Abundance of <i>Bacteroidetes</i> was negatively correlated with LDL-C; Abundance of <i>Tenericutes</i> was negatively correlated with hip circumference and total cholesterol, positively correlated with HDL-C and cake intake; <i>Actinobacteria</i> was positively correlated with BMI and folic acid intake, negatively correlated with oil intake. <i>Firmicutes</i> was negatively correlated with beverage and alcohol intake. <i>Spirochaetae</i> was negatively correlated with fungus, fruits, beans, vitamin C, dietary fiber, and calcium. <i>Fusobacteria</i> was positively correlated with beans intake, and was negatively correlated with fat intake. <i>Proteobacteria</i> was positively correlated with tuber crops intake. <i>Synergistetes</i> was positively correlated with cholesterol, nicotinic acid, and selenium intake. <i>Deferribacteres</i> was negatively correlated with magnesium intake. <b>Conclusions:</b> At the phylum and genus level, the structure and diversity of intestinal microbiota of T2DM and IGR was altered, the number of OTUs, the relative abundance, and diversity were all decreased. The gut microbiota of the newly diagnosed T2DM, IGR, and NC were related to age, blood lipids, BMI, blood pressure, and dietary nutrient intake. Unbalanced nutrient intake in the three groups may affect the structure and abundance of the gut microbiota, which may play a role in the occurrence and development of T2DM.