Because of increasing interest in the functional surfaces including micro- or nano-patterns, the mass production of such surfaces has been actively researched. Both conventional injection molding (CIM) and injection/compression molding (ICM) of micro-patterns were investigated in the present study. The molding subject is a multi-scale structure that consists of a macro-scale thin plate and micro-scale patterns formed regularly on its surface. The transcription ratios of micro pattern made by CIM and ICM for different flow length were experimentally measured, and the origin of the obtained results was identified through numerical analysis. It was found that the cavity pressure and polymer temperature are the most important factors for micro-pattern filling; in particular, the polymer temperature is the key factor determining the transcription ratio. It was also found that the difference in CIM and ICM micro-pattern transcription ratios originates from the differences in the cavity pressure history if other molding conditions are the same.