Fine bubbles have been applied in many fields; however, the controllable preparation of monodispersed fine bubbles remains a challenge. In this study, a three-dimensional (3-D) flow-focusing microfluidic device was designed. Compared with bubble formation in one-dimensional (1-D) and two-dimensional (2-D) flow-focusing, the 3-D flow-focusing microchannel owns the features of making bubbles with much smaller sizes and wider operation range. Four different gas–liquid flow regimes (squeezing, squeezing-dripping transition, dripping, and jetting) and three different gas–liquid dispersion states (mono-dispersion, bi-dispersion, and poly-dispersion) were observed in the 3-D flow-focusing microchannels. Importantly, the bi-dispersion in the squeezing-dripping transition regime experimentally verified that the squeezing and viscous shearing mechanisms separately control bubble formation in the transition region based on the time sequence. The intrinsic reason for poly-dispersion in the squeezing-dripping transition and jetting regimes was revealed. Finally, a mathematical model is proposed to predict the bubble size in the flow-focusing microchannels.