Submicron emulsions could be produced via the tip-streaming process in a flow-focusing microfluidic device. In this article, the stability of the liquid cone and thread for tip-streaming mode could be significantly improved by employing a three-dimensional flow-focusing device, in which the hydraulic resistance was adjusted by modulating the channel heights in the flow focusing area, orifice, downstream and dispersed phase inlet channel. The pressure range for tip-streaming mode was enlarged significantly compared with two-dimensional flow-focusing devices. Therefore, monodisperse emulsions were produced under this tip-streaming mode for as long as 48 hours. Furthermore, we could control the size of emulsion drops by changing the pressure ratio in three-dimensional flow-focusing devices while the liquid cone was easily retracted during the adjustment of pressure ratio in two-dimensional flow-focusing devices. Furthermore, using the uniform submicron emulsion droplets as confining templates, polyethylene glycol (PEG) particles were produced with a narrow size distribution at the sub-micrometre scale. In addition, magnetic nanoparticles were added to the emulsion for magnetic PEG particles, which can respond to magnetic field and would be biocompatible.