This original research developed a multifunctional calcium delivery system by fabricating a fructooligosaccharide–Larimichthys crocea peptide (FOS-LCP) copolymer using a food-grade wet-heating method. The copolymer exhibited significantly improved calcium-binding capacity, digestive stability, and resistance to dietary inhibitors such as phytates and oxalates, resulting in enhanced calcium uptake and intestinal transport compared with peptide alone. In cellular and intestinal models, FOS-LCP promoted calcium absorption primarily via paracellular pathways. Using bone marrow mesenchymal stem cells from calcium-deficient mice, the study further demonstrated that FOS-LCP enhanced osteogenic differentiation, increased mineralization and osteogenic marker expression, while simultaneously suppressing adipogenic differentiation and lipid accumulation. These effects were mediated through activation of the Wnt/β-catenin pathway and inhibition of PPARγ-driven adipogenesis. The findings support FOS-LCP as a promising functional calcium delivery system that not only improves calcium bioavailability but also rebalances bone-lipid metabolism, offering potential applications in functional foods and precision nutrition.