Recently, the good physical and chemical properties, well-defined pore architectures, and designable topologies have made microporous organic networks (MONs) excellent potential candidates in high-performance liquid chromatography (HPLC). However, their superior hydrophobic structures restrict their application in the reversed-phase mode. To solve this obstacle and to expand the application of MONs in HPLC, we realized the thiol-yne "click" postsynthesis of a novel hydrophilic MON-2COOH@SiO2-MER (MER denotes mercaptosuccinic acid) microsphere for reversed-phase/hydrophilic interaction mixed-mode chromatography. SiO2 was initially decorated with MON-2COOH using 2,5-dibromoterephthalic acid and tetrakis(4-ethynylphenyl)methane as monomers, and MER was then grafted via thiol-yne click reaction to yield MON-2COOH@SiO2-MER microspheres (5μm) with a pore size of ~1.3nm. The -COOH groups in 2,5-dibromoterephthalic acid and the post-modified MER molecules considerably improved the hydrophilicity of pristine MON and enhanced the hydrophilic interactions between the stationary phase and analytes. The retention mechanisms of the MON-2COOH@SiO2-MER packed column were fully discussed with diverse hydrophobic and hydrophilic probes. Benefiting from the numerous -COOH recognition sites and benzene rings within MON-2COOH@SiO2-MER, the packed column exhibited good resolution for the separation of sulfonamides, deoxynucleosides, alkaloids, and endocrine-disrupting chemicals. A column efficiency of 27,556 plates per meter was obtained for the separation of gastrodin. The separation performance of the MON-2COOH@SiO2-MER packed column was also demonstrated by comparing with those of MON-2COOH@SiO2, commercial C18, ZIC-HILIC, and bare SiO2 columns. This work highlights the good potential of the thiol-yne click postsynthesis strategy to construct MON-based stationary phases for mixed-mode chromatography.