A glass liquid–liquid extraction (LLE) microchip with three parallel 3.5cm long and 100μm wide interconnecting channels was optimized in terms of more environmentally friendly (greener) solvents and extraction efficiency. In addition, the optimized chip was successfully hyphenated with nano-liquid chromatography with ultraviolet and mass spectrometric detection (nanoLC–UV–MS) for on-line analysis. In this system, sample pretreatment, separation and detection are integrated, which significantly shortens the analysis time, saves labor and drastically reduces solvent consumption. Strychnine was used as model analyte to determine the extraction efficiency of the optimized 3-phase chip. Influence of organic solvent, pH of feed phase, type of alkaloid, and flow rates were investigated. The results demonstrated that the 3-phase chip nanoLC–UV/MS hyphenation combines rapid (∼25s) and efficient (extraction efficiency >90%) sample prep, with automated alkaloid analyses. The method was applied to real samples including Strychnos nux-vomica seeds, Cephaelis ipecacuanha roots, Atropa belladonna leaves, and Vinca minor leaves.