Generating droplets via microfluidic chips is a promising technology in microanalysis and microsynthesis. To realize room-temperature ionic liquid (IL)-water two-phase studies in microscale, a water-immiscible IL was employed as the continuous phase for the first time to wrap water droplets (either plugs or spheres) on flow-focusing microfluidic chips. The IL, 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]), could wet both hydrophilic and hydrophobic channel surfaces because of its dual role of hydrophilicity/hydrophobicity and extremely high viscosity, thus offering the possibility of wrapping water droplets in totally hydrophilic (THI), moderately hydrophilic (MHI), and hydrophobic (HO) channels. The droplet shape could be tuned from plug to sphere, with the volume from 6.3 nL to 65 pL, by adding an orifice in the focusing region, rendering the hydrophilic channel surface hydrophobic, and suppressing the Uw/UIL ratio below 1.0. Three different breakup processes were defined and clarified, in which the sub-steady breakup and steady breakup were essential for the formation of plugs and spheric droplets, respectively. The influences of channel hydrophilicity/hydrophobicity on droplet formation were carefully studied by evaluating the wetting abilities of water and IL on different surfaces. The superiority of IL over water in wetting hydrophobic surface led to the tendency of forming small, spheric aqueous droplets in the hydrophobic channel. This IL-favored droplet-based system represented a high efficiency in water/IL extraction, in which rhodamine 6G was extracted from aqueous droplets to [BMIM][PF6] in the hydrophobic orifice-included (HO-OI) channel in 0.51 s.