The immobilized κ-carrageenase MCNF was developed by synergistic integration of κ-carrageenase, calcium phosphate crystals, and magnetic nanoparticles. MCNF outperformed free κ-carrageenase in terms of optimal temperature, thermostability (45–55 °C), stability (pH 6.0 and 12.0), and storage stability. Furthermore, MCNF was extremely reusable and easy to separate from the reaction system. MCNF's enzymatic breakdown of κ-carrageenan resulted in a tetrasaccharide that competitively inhibited pancreatic lipase (PL). Fluorescence titration experiments showed that κ-carrageenan tetrasaccharide altered the microenvironment of PL by causing static bursting of its intrinsic fluorescence. The circular dichroism experiment demonstrated that adding κ-carrageenan tetrasaccharide reduced α-helix content and increased β-sheet content in PL's secondary structure. Molecular docking and dynamics simulation research suggested that the κ-carrageenan tetrasaccharide could form a stable complex with PL, entering its hydrophobic cavity and occupying its active site, reducing PL's catalytic activity. κ-Carrageenan tetrasaccharide could inhibit PL, making it a promising therapeutic agent for obesity prevention and treatment.