Extraction of trace contaminants from fatty food matrices is challenging in food analysis. Herein, a new ionic liquid-based one-, two-, three-phase transition microextraction (IL-OTTPTME) was proposed to efficiently extract trace targets while simultaneously eliminating lipid co-extractives. The method performance was illustrated through the determination of chrysoidine in fatty soybean products using high-performance liquid chromatography-ultraviolet/visible detection. The strong interactions and infinite contact between IL and chrysoidine in the one-phase system ensured ultra-high extraction efficiency (∼100 %). Density functional theoretical calculations confirmed the presence of strong hydrogen bonding and π-π interactions. The formation of the three-phase system during extraction could completely eliminate lipid co-extractives. The IL-OTTPTME integrated extraction, enrichment and cleanup steps into one step, making it rapid and extremely easy to operate. The method had a wide linear range of 0.5–5000 μg/kg and low limit of detection (0.15 μg/kg). It also had satisfactory relative recoveries (95.1 %-104.0 %) and low RSDs (≤5.0 %, n = 5).