This study aimed to investigate effects of long-term probiotic supplementation on gut microbiota and growth performance in health weaned piglets. The non-probiotic group (N-PrB) was fed only a basal diet, while the probiotic group (PrB) was fed a basal diet + probiotic combination (E. faecium 1.6 × 108 CFU/g, B. subtilis 2.0 × 108 CFU/g, S. cerevisiae 3.0 × 108 CFU/g). The probiotics combination was provided to the PrB, mixing with the basal diet in 5 kg/ton. As a result, the PrB exhibited significantly improved weight gain compared to the N-PrB (p = 0.00991). In the gut microbiome analysis, the PrB exhibited a significant increasing tendency of α-diversity compared to those of the N-PrB (p < 0.01). In the bacterial relative abundance changes in bacteria comprising the gut microbiota, Ruminococcaceae (p = 0.00281) and Prevotella (p = 0.00687) tended to significantly increase in the PrB, but decreased in the N-PrB. The Eubaterium coprostanoligenes group exhibited an increasing tendency in both groups, but tended to increase more significantly in the PrB compared to the N-PrB (p = 0.00681). Muribaculaceae tended to significantly increase in the N-PrB, but decreased in the PrB (p = 0.002779). In this study, significant differences on the gut microbiome were found according to the probiotics supplementation in the weaned piglets and these gut microbiome changes appeared to improve the growth performance.