Boronate affinity materials have been widely studied in separation science, chemical sensing, drug delivery and nanomedicine due to their unique recognition mechanism towards cis-diol-containing biomolecules (cis-diols). In this paper, a new phenylboronic acid (PBA)-functionalized silica particle was prepared by one-pot synthetic strategy based on a PBA-coupled silane reagent, which was synthesized using 1,3,5-benzenetricarboxaldehyde as a spacer arm to covalently link 3-aminophenylboronic acid and 3-aminopropyltriethoxysiliane. Such PBA-functionalized silica particles displayed wrinkle shape with large surface area of 192 m2 g−1, resulting in its high binding capacities of 480 µmol g−1 for catechol and 63 µmol g−1 for adenosine. Moreover, the PBA-functionalized silica particles could rapidly extract the cis-diols in 10 min with a high binding recovery of 83–92%, much higher than its control polymers (1 ~ 47%). In addition to the good extraction performances, the PBA-functionalized silica particles also exhibited fluorescence responses to the cis-diols using two different excitation lights at 300 nm and 470 nm, giving emission lights at 379 nm and 631 nm, respectively, whose fluorescence-responsive mechanism was preliminarily studied. In summary, the developed boronate affinity silica particles can be used not only for the solid-phase extraction of cis-diols, but also to report the recognition events through the fluorescence signals, providing an idea to develop multi-functional boronate affinity materials for simultaneous enrichment and detection of cis-diols in biological samples.