Galacto-oligosaccharides (GOS) are recognized prebiotics with extensive applications in animal nutrition. This study aimed to elucidate the effects of chlortetracycline (CTC) supplementation alongside GOS on growth performance, intestinal morphology, and microbiota composition in weaned piglets. A total of 72 weaned piglets [(Duroc × (Landrace × Yorkshire)] with an initial body weight of 7.64 ± 0.15 kg were randomly assigned to three dietary treatments: a corn-soybean meal-based diet (CON), a corn-soybean meal-based diet supplemented with chlortetracycline (CTC) at 75 mg/kg, and a diet with 1500 mg/kg GOS. The experiment spanned 14 days, divided into early (1-7 days) and late (7-14 days) stages. The results indicated that the GOS group exhibited a significant increase in body weight (BW) by day 14 and improved average daily gain (ADG) from day 1 to 14, alongside a decreased feed-to-gain ratio and diarrhea incidence ( < 0.05). Notably, GOS supplementation enhanced the villus height of the jejunum and increased the ratio of villus height to crypt depth compared to the CON group, although no significant differences were observed between GOS and AntB groups. Additionally, the number of goblet cells in the colonic crypts increased significantly with GOS supplementation. High-throughput 16S rRNA gene sequencing revealed an increased relative abundance of Firmicutes in the GOS group, coupled with a decrease in Bacteroidetes and Spirochaetota. Beneficial bacteria such as Lactobacillus and Faecalibacterium were significantly enriched, while potentially pathogenic bacteria, including Clostridium_sensu_stricto_1 and Treponema, were reduced. In summary, dietary GOS supplementation can enhance beneficial microbiota while diminishing harmful species, thereby improving intestinal morphology and growth performance in weaned piglets. Consequently, GOS emerges as a promising alternative to in-feed antibiotics in contemporary animal husbandry.