Microbubble streaming in a microfluidic device has been increasingly studied and used in recent years, due to its unique flow pattern that can promote mixing, sort particles and trap particles in microscale flows. However, there have been few numerical studies of this subject. We performed a 3D direct simulation of a cylindrical-shaped microbubble, trapped in a pit of a microchannel and sandwiched between two parallel plates, vibrated by pressure oscillation. Our simulation was able to reproduce the experimentally observed relation between the bubble protrusion depth and the vortex pattern: As the bubble protrusion depth increased, new vortices emerged and grew larger. Our investigation of the streamlines near the bubble interface indicates that the number of non-spherical nodes in the bubble interface is closely related to the flow pattern in the liquid phase. It was also validated by our simulation that the flow velocity showed an exponentially decaying trend as the radial distance outward from the vortex center. Our numerical model was also used to investigate the effects of surface tension and channel size on the vortex pattern. Larger surface tension or smaller channel size showed a similar effect as the increased protrusion depth induced more vortices.