Sialoglycoproteins, rich in sialic acid, are dietary mucins with potential effects on human nutrition and health. This study examined the influence of sialoglycoprotein from edible bird's nest (EBN), desialylated edible bird's nest (ABN), and N-acetylneuraminic acid (Neu5Ac) on the proliferation of probiotics and fecal bacteria from pregnant women in vitro. EBN and Neu5Ac, compared with ABN, were more effective in promoting the growth of beneficial gut microbiota, particularly Lactobacillus and Bifidobacterium. EBN, with intact sialic acid, markedly enhanced the growth of Akkermansia muciniphila. Within 24 h, EBN stimulated short-chain fatty acid production during in vitro fermentation of fecal samples from healthy and late-stage pregnant women. EBN also modulated the microbial community, decreasing the relative abundance of potentially pathogenic bacteria, including Enterobacteriaceae and Klebsiella, and increasing the abundance of beneficial genera, such as Bacteroides and Faecalibacterium. Notably, EBN was superior to ABN in suppressing pathogenic bacteria and promoting probiotic proliferation. In contrast, monomeric Neu5Ac failed to decrease Klebsiella populations and increased Enterococcus faecium in fecal samples from elderly pregnant women. Overall, protein-bound Neu5Ac exhibited greater prebiotic activity than the free monomeric form.