<p>Metal organic frameworks (MOFs) exhibit significant application potential in separation science, showing particular promise as chromatographic packing materials. To address the problems of low mechanical strength, poor aqueous stability, complex synthesis procedures and high consumption of organic solvents in traditional MOF-based stationary phases, this study adopted a green and facile strategy employing water as the main solvent and room-temperature stirring combined with water-bath heating to prepare a Zr-MOF hybrid silica stationary phase. Specifically, aminated silica was first modified with 2,5-furandicarboxylic acid as a bio-renewable organic building block to obtain carboxyl-functionalized silica, followed by its reaction with ZrOCl₂·8H₂O as the metal source to yield the Zr-FDCA-MOF@SiO₂ stationary phase. The separation performance of Zr-FDCA-MOF@SiO₂ was systematically investigated by selecting various substances such as nucleosides, sulfonamides, antibiotics, vitamins, polycyclic aromatic hydrocarbons and positional isomers as target analytes, and the chromatographic retention mechanism was explored. The practical applicability was verified by the analysis of real pharmaceutical and food samples. The results showed that the as-prepared Zr-FDCA-MOF@SiO₂ possessed favorable mechanical strength, adequate aqueous stability, satisfactory separation efficiency with acceptable repeatability, enabling effective separations of analytes with multiple polarities. This study establishes an environmentally friendly synthetic route to fabricate an efficient MOF based stationary phase using a bio-renewable ligand, which has clear academic significance and good potential for practical application.</p> Graphical abstract <p> This work presents a mild aqueous route to Zr-FDCA-MOF@SiO₂ for high-performance multi-mode chromatographic separation of diverse analytes.</p> <p></p>