Droplet-based microfluidic chips have shown great advantages in fields of chemical and biological researches. Based on the different wettabilities of water, IL (ionic liquid, 1-butyl-3-methylimidazolium hexafluorophosphate) and soybean oil in hydrophobic channels, three kinds of droplet pairs (including an alternating water-IL droplet chain, connected water-IL droplet pairs and separated water-IL droplet pairs) were generated for the first time in soybean oil on microfluidic chips containing double flow-focusing regions. The influences of fluid flow rate and channel geometry on droplet pair formation were carefully studied.