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Early mammal gut microorganism colonization affects host health, the feed conversion rate, and production performance. Herein, we explored how fecal microbiota develops and the interactions between microorganisms and nutrients. The lambs were separated from ewes at 7 days old, artificial feeding with milk replacer completely replaced lactation, and the starter diet was added. At 21 days old, the lambs were fed with complete starter and milk replacer was stopped. At day 7, 21, 35, and 49 after birth, fecal samples were collected. Then 16S rRNA gene sequencing in the fecal samples revealed that the alpha diversity increased significantly with age. Principal coordinates analysis showed clear clustering by age (p < 0.05). At the genus level, the relative abundance of 8 genera declined, 12 genera increased (p < 0.1), and 4 genera changed dramatically with age (p < 0.05). The apparent digestibility of dry matter, protein, fat, neutral detergent fiber, and acid detergent fiber significantly decreased by 21.77%, 23.15%, 23.62%, 19.38%, and 45.24%, respectively, from 7 to 35 days of age (p < 0.05), but not thereafter (p > 0.05). Fecal nutrient contents affected the abundance of bacterial genera (p < 0.05). Enterobacteriaceae_unclassified, Clostridium XlVb, Bifidobacterium, and other genera had no relationship with the fecal nutrient content; however, they were closely related to nutrient intake and digestibility, possibly promoting nutrient digestion. Our results suggested that nutrient digestion of young lambs changed rapidly, which was closely related to intestinal microbial colonization.