An understanding of the nutrient utilization characteristics of pigs with different feed efficiencies (FEs) will help us to develop new strategies to reduce the costs of pig production. In this study, we selected pigs with a range of FEs according to two feed conversion ratio models: the feed intake (FI) model, where pigs had the same average daily gains (ADGs) but different FIs, and the ADG model, where pigs had the same FIs but different ADGs. High-FE pigs had a higher abundance of short chain fatty acid (SCFA)-producing bacteria (Lachnospiraceae, Clostridiaceae_1, and Coriobacteriaceae) in their caecum in the FI model, and low-FE pigs had a higher abundance of two families (Bacteroidales_S24_7_group and Peptococcaceae) and two genera (Anaerotruncus and Candidatus_Soleaferrea) in both models. By contrast, high-FE pigs had more goblet cells and higher mRNA expression of insulin-like growth factor 1 (IGF-1) in the FI model, and higher mRNA expression of occludin but lower expressions of adenosine monophosphate-activated protein kinase (AMPK)-α2 and peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC1α) in the ADG model. These findings suggest that the presence of SCFA-producing bacteria in the caecum and increased muscular growth may contribute to the high FE of low-FI pigs, while improved intestinal functions and decreased mitochondrial activity in the skeletal muscle are related to the high FE of high-ADG pigs.