Dietary supplementation with Lactobacillus can improve the intestinal microbial balance and exerts beneficial effects on pig health. However, whether these effects in pigs show differences between the sexes remains poorly understood. Therefore, we analyzed the sex-dependent patterns in the fecal microbiota after dietary supplementation with Lactobacillus acidophilus ZLA012 through high-throughput sequencing, determined the metabolomic profile of serum in barrows (immature castrated males) and gilts (sexually immature females) through nontargeted liquid chromatography-mass spectrometry, and measured the levels of various hormones, such as insulin, growth hormone, serotonin, triiodothyronine, and thyroxine. Lactobacillus supplementation resulted in more obvious effects on the microbial diversity and composition in barrows than in gilts. Specifically, supplementation with L. acidophilus ZLA012 significantly increased the abundance of the phylum Bacteroidetes and decreased that of Firmicutes in barrows. In contrast, more notable effects on metabolites, particularly those involved in lipid metabolism and glycerophospholipid metabolism, were observed in gilts than in barrows after Lactobacillus supplementation. Megasphaera, Dialister, Gemmiger, Faecalibacterium, Bulleidia, and Prevotella were the core functional genera associated with the significantly affected metabolites, which are involved in the biosynthesis, degradation, and elongation of fatty acids. L. acidophilus ZLA012 treatment increased the serum insulin, total bile acid, lipoprotein lipase, and nicotinamide adenine dinucleotide (NAD)(+) levels in gilts, whereas higher serotonin levels were found in barrows than in gilts. The results indicated that the separate housing of barrows and gilts might be beneficial for targeted dietary supplementation and application of Lactobacillus in pig production.