Sialyloligosaccharides, critical components of human milk oligosaccharides, are pivotal for infant immunity and development. Recent advances have identified sialidases with trans-sialylation activity as promising biocatalysts for cost-effective sialyloligosaccharide synthesis using economical substrates. Herein, we report a novel sialidase (KsSiase1) from Kribbella sp. ALI-6-A with enhanced catalytic properties and broad substrate specificity, showing preferential hydrolysis: α2,3 > α2,6 > α2,8. The enzyme demonstrated robust trans-sialidase activity, achieving 3.40 g/L sialyloligosaccharide production using 0.5 U/mL KsSiase1, 6% lactose, and 8% cGMP. Implementing a direct-fed enzymatic strategy in raw milk with 1 U/mL KsSiase1 and 6% cGMP, we achieved in situ sialyloligosaccharide enrichment (2.49 g/L) while concomitantly reducing lactose. This biocatalytic system establishes a sustainable, scalable platform for functional food production, merging lactose valorization with sialyloligosaccharides biosynthesis through enzyme-substrate adaptability, addressing both industrial demands and nutritional needs in infant formula development.