Objective The aim of this experiment was to explore the effect and mechanism of intestinal microbiota on shaping the growth performance by fecal microbiota transplantation from pigs to pseudo-germ-free mice. Methods Thirty-six barrows with a similar initial body weight of 30 kg were raised for 42 days (ad libitum) within individual metabolic cages. Feed intake and body weight of each pig were recorded every week to calculate the feed conversion rate and average daily gain. At the end of the experiment, feed conversion ratio and average daily gain were integrated to divide the pigs into 3 groups, namely, high growth performance (HP), moderate growth performance (MP) and low growth performance (LP) groups. Feces were collected to calculate the total intestinal nutrient digestibility and prepare for fecal microbiota transplantation to pseudo-germ-free mice, which were induced with several antibiotics for four weeks. Fecal microbiome structure was assayed by profiling V3-V4 region of the 16S rRNA gene. Results Fecal microbiota transplantation from pigs to pseudo-germ-free mice resulted in reappearance of the original phenotype. Compared with the LP pigs, the microbial species richness and microbial diversity in feces were higher in the HP pigs. The HP pigs had improved digestibility of gross energy ( P = 0.01) and higher abundance of Methanobrevibacter. Enterococcus and Akkermansia were also more abundant in the recipient pseudo-germ-free mice from the HP pigs which may be correlated with a high energy utilization. Conclusions Fecal microbiota transplantation from pigs to mice results in reappearance of the original phenotype and microbial species richness, microbial diversity, and their growth ability. Different nutritional metabolism is shown among pigs with different feed efficiency and the HP pigs have improved energy utilization ( P =0.01). At the same time, the bacteria correlated with high energy utilization are more abundant in feces of HP pigs than in LP pigs.