The conventional finite element method was employed to study the relationship between melt filling and air accumulation in micro-cavities. The variational equation for melt flow with slip boundary condition and air resistance was generalized based on Galerkin principle. To investigate the effect of air accumulation, the governing equation for air flow inside runner was established by dimensionless method. An iterative approach was proposed to solve the coupled melt flow problem and air flow problem. Numerical results show that air accumulation can affect the melt filling in micro-cavity, and closely depends on injection speed. Adjusting branch runner distribution can improve the flow balance, which was convinced by a real micro-part manufacturing.