In this study, interactive effects of microstructure and cavity dimension on the filling behaviors in micro coining were investigated. The results indicate that the filling ability is dependent on both the cavity width t and the ratio of cavity width to grain size t/d strongly. The critical ratio t/d for the worst filling ability increases with cavity width t and tends to disappear when the cavity width t increases to 300 μm. A polycrystalline filling model considering the friction size effect, effect of constrained grains by the tools, grain size, cavity width and ratio of cavity width to grain size is proposed to reveal the filling size effect in micro coining. A quasi in-situ Electron Backscatter Diffraction (EBSD) method is proposed to investigate filling mechanism in micro coining. When several grains across the cavity width, each grain deforms heterogeneously to ordinate the deformation compatibility. When there is only one grain across the cavity width, the grain is fragmented into several smaller grains with certain prolongation along the extrusion direction to coordinate the deformation in the cavity. This is different from the understandings before. Then the filling deformation mechanism is revealed by a proposed model considering the plastic flow in micro coining.