The occurrence of microcystins (MCs) during harmful algal blooms (HABs) represents a major threat to freshwater environments. In this work, a novel surface amphiphilic hybrid porous polymers based on cage-like organosiloxanes (PCSs) was prepared for the enrichment of MCs. The copolymerization of bifunctional amphiphilic monomers, 2-methacryloyloxyethyl phosphorylcholine (MPC) and N-benzylquininium chloride (BQN), with the cross-linker methacryl substituted polyhedral oligomeric silsesquioxane (POSS) was achieved in an ionic liquid-based porogenic medium. The hierarchical porous structure, a variety of surface functional groups and weak hydrophilicity were well characterized on the prepared materials using scanning electron microscopy, nitrogen adsorption/desorption analysis, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, zeta potential analysis and water contact angle testing, respectively. The as-prepared surface amphiphilic PCSs was used as an adsorbent for pipette tip solid-phase extraction (PT-SPE) to enrich microcystins (MCs) from surface waters before their analysis by capillary electrochromatography (CEC) and liquid chromatography-mass spectrometry (LC-MS). Under the optimal conditions, the established PT-SPE-LC-MS method exhibited a wide linear range (10–10,000 ng L−1), low limits of detection (4.0–8.0 ng L−1) and satisfactory recoveries (89.5–102.8 %) for MCs. An adsorption mechanism involving electrostatic interactions, hydrogen bonding, hydrophilic interactions, and π-π stacking has been proposed. The findings suggest that the use of surface amphiphilic PCSs materials as adsorbents in the PT-SPE platform facilitates efficient enrichment of MCs for subsequent chromatographic analysis. These investigations offer a new perspective on the simple and uncomplicated pretreatment of complex environmental samples.