Improving feed efficiency (FE) plays an essential role in the economic and environmental sustainability of the swine industry. Genetic selection based on estimated breeding values for feed conversion ratio (EBV_FCR) can effectively improve FE. This study investigated the growth performance, nutrient and energy digestibility, activity of hydrolyses, expression of nutrient transporters and tight junction proteins, and gut microbiome of nursery pigs selected for high and low feed efficiency. A total of 128 pigs weaned at 21+2 days were selected from parents with low or high EBV_FCR, representing low (n=64) and high (n=64) FE groups. Pigs were fed corn-soybean meal-based diets in a two-phase feeding program for four weeks under similar rearing conditions. The results revealed no differences in average daily feed intake, average body weight gain, feed conversion ratio (FCR), and energy and nutrient digestibility between the two groups. Moreover, the two groups had no differences in the maximal activity of alkaline phosphatase, sucrase, maltase, and maltase-glucoamylase (P > 0.05). SGLT1, ASCT2, PepT1, EAAC1, and BoAT1 mRNA abundances were not different between the two groups (P > 0.05). There were also no significant differences in claudin-1 and ZO-1 protein abundances in the jejunum between the two pig groups. The two pig groups had similar fecal microbial taxonomic composition and function. However, the high FE group had a higher relative abundance of Lactobacillus in the jejunum, and the low FE group was associated with higher relative abundances of Prevotella, Blautia and Faecalibacterium in the cecum and colon. The high-efficiency pig group had higher species evenness, and there was a trend (P < 0.084) for beta diversity difference, indicating that high-efficiency pigs might have a healthier gut environment. In conclusion, nursery pigs selected for high and low feed efficiency based on parents’ EBV_FCR did not differ in growth performance, nutrient digestibility and absorptive capacities, fecal microbiota composition and functions. Microbiota differences were present for the jejunum, cecum and colon of these two pig groups suggesting different functionality that need to be further investigated.