Hexagonal boron nitride (h-BN) is considered as an ideal substrate material for new electronic devices and nano-electromechanical (NEMS) devices, owing to its hexagonal network lattice structure and high chemical and mechanical stability. It can be used to seal gas with a long-term stability, and then has a big potential in further applications in electronics and NEMS. Recently, researchers have discovered that hydrogen atoms can penetrate multiple layers of h-BN non-destructively, forming the bubbles between layers, which can be used as NEMS devices. In this article, we investigate the effect of hydrogen plasma treatment duration on the size of h-BN bubbles. It is found that the size of bubbles becomes larger with the increase of treatment time while their distribution density decreases. It is also observed that the prepared h-BN bubbles have similar morphological characteristics, which are related to Young’s modulus of h-BN and interlayer van der Waals interaction. With the help of force-displacement curve measurement, it is obtained that the internal pressure is about 1—2 MPa for micro-sized bubbles, while the internal pressure of nano-sized bubbles can reach a value of GPa.