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The intestine is a complex micro-ecosystem, and its stability determines the health of animals. Different dietary nutritional levels affect the intestinal microbiota and health. In this study, the nutritional levels of energy and protein in the diet of goats were changed, and the body weight was measured every 15 days. In the late feeding period, 16 S rRNA sequencing technology was used to detect the content of microorganisms. A meteorological chromatograph was used to detect volatile fatty acids in the cecum and colon of goats. In the feeding stage, reducing the nutritional level of the diet significantly reduced the weight of the lamb (<i>p</i> < 0.05). In the cecum, the abundance of potentially harmful bacteria, such as <i>Sphingomonas</i>, <i>Marvinbryantia,</i> and <i>Eisenbergiella,</i> were significantly enriched in goats fed with the standard nutritional level diets (<i>p</i> < 0.05). Additionally, the contents of acetate (<i>p</i> = 0.037) and total VFAs (<i>p</i> = 0.041) increased. In the colon, the abundance of SCFAs-producing bacteria, such as <i>Ruminococcaceae</i>, <i>Christensenellaceae,</i> and <i>Papillibacter,</i> decreased as the nutritional level in the diet increased (<i>p</i> < 0.05). In conclusion, the increase in nutritional level could affect the growth performance and composition of intestinal microbiota.