Herein we investigate the formation of aromatic organic nanoparticles in a three-dimensional (3D) hydrodynamic flow focusing microfluidic device. We demonstrate a microfluidic based solvent/non-solvent exchange technique that enables controllable formation of aromatic nanoparticles with tunable size and size distribution. The 3D focusing is achieved by hydrodynamically focusing the sample stream with sheathed streams in both horizontal and vertical directions, and solvent/non-solvent exchange happens between the solvent contained sample stream and non-solvent contained horizontally sheathed streams. The 3D focusing effect was visualized using florescence confocal microscopy and the dynamics of solvent (DMF) depletion in the focused stream was calculated using a finite element computation software package COMSOL Multiphysics. By analyzing the results of self-assembled aromatic nanoparticles in the microfluidic device, we find that the speed of DMF depletion strongly influences the size and size distribution of self-assembled aromatic nanoparticles, and a rapid depletion of DMF is critical for achieving small aromatic nanoparticles with narrow size distribution. This work suggests that our 3D hydrodynamic flow focusing microfluidic device with the ability to precisely control the convective-diffusion process, and continuously vary the fluid flow conditions is promising for studying the formation of nanomaterials.