In this work, an ionic liquid-based ultrasonic-assisted extraction (ILUAE) method was developed to extract caffeoylquinic acids (CQAs) from Flos Lonicerae Japonicae (FLJ). ILUAE parameters were optimized by response surface methodology, including IL concentration, ultrasonic time, and liquid–solid ratio. Optimized ILUAE approach gained the highest extraction yields of 28.53, 18.21, 3.84 mg/g for 3-O-caffeoylquinic acid (C1), 3,5-di-O-caffeoylquinic acid (C2), 3,4-di-O-caffeoylquinic acid (C3), respectively. C1–C3 are the three most abundant CQAs compounds in FLJ. The method showed comparable extraction yield and shorter extraction time compared with conventional extraction techniques. Subsequently, an aqueous two-phase system (ATPS) was applied in extraction solutions. Two trace CQAs, 5-O-caffeoylquinic acid (C4) and 4,5-di-O-caffeoylquinic acid (C5), were significantly enriched with signal to noise values increasing from less than 10 to higher than 1475. The results indicated that ILUAE and ATPS are efficient and environmentally-friendly sample extraction and enrichment techniques for CQAs from herbal medicines.