In this paper, we investigated the effects of a diet with a moderate reduction of dietary crude protein (CP) level, supplemented with five crystalline amino acids (Lys, Met, Thr, Try, and Val), on the growth, metabolism, and fecal microbiota of Sushan nursery pigs. Seventy Sushan nursery pigs with an average body weight of 19.56 ± 0.24 kg were randomly allocated to two experimental dietary treatments: 18% CP (high protein; group HP), and 15% CP (low protein; group LP). We found that the differences in the two diets had no significant effect on the growth performance of Sushan nursery pigs. Nursery pigs on the 15% CP diet showed significantly improved protein, amino acid, and energy utilization. Furthermore, the LP diet cloud optimized the gut microflora composition to some extent. The functional structure of bacterial communities implied improved metabolic capabilities in group LP. Additionally, correlation analysis between fecal microbiota and metabolic profiles confirmed that the increase of beneficial bacterial in the feces was beneficial to the health and metabolism of the nursery pigs. In conclusion, a moderate reduction in the dietary protein level can improve growth and metabolism due to the improvement of intestinal microbiota in Sushan nursery pigs. This finding could provide useful reference data for the application of a different nutrition strategy in indigenous pig production.