In this study, three yeast α-mannans (LZ-MPS, MC-MPS, and G-MPS) were extracted from different sources of Kluyveromyces marxianus. The total sugar content of the three α-mannans ranged from 91.13–97.10%, whereas no proteins were detected. A structural arrangement was proposed using ultraviolet spectroscopy, Fourier-transform infrared spectroscopy, and one-dimensional and two-dimensional nuclear magnetic resonance. The main chain of the three yeast α-mannans was formed by a →6)-α-D-Manp-(1→ unit, which was slightly different from the repeating unit of the branch structure. The prebiotic potential of LZ-MPS, MC-MPS, and G-MPS was assessed using in vitro fermentation with pure and faecal cultures. The three yeast α-mannans could be utilised as substrates for the growth of Lactobacillus and Lactococcus strains. In addition, the three yeast α-mannans markedly regulated the intestinal microbiota composition by increasing the relative abundances of Bacteroides, Parabacteroides, and Phascolarctobacterium and decreasing the abundance of pathogenic bacteria.