In micro injection molding, the cavity thickness and surface roughness are the main effects factors of polymer flow in the die designing and affect the quality of molded products significantly. In this study, the effects of cavity thickness and roughness of cavity surface were investigated mainly on polymer flow during molding and on the roughness of molded products. The parts were molded in the cavities with the thickness from 0.05 mm to 0.25 mm and surface roughness from Ra = 46.55 nm to Ra = 462.57 nm, respectively. The filling integrities and roughness replication ratio of molded parts were used to evaluate the statements of polymer flow and microstructure replication during micro injection molding, respectively. The results showed that the filling integrity changing trends in the thinner cavities were obviously different or even opposite to those in the thicker cavities with the changing of cavity surface roughness instead of single trend in the conventional studies. For each cavity surface roughness, the filling integrity showed an upward trend with the increasing cavity thickness. In different cavity thickness, the maximum gap of filling integrity was 23.76 mm, reaching 544.94% from 0.05 mm to 0.25 mm. Additionally, the surface roughness ratio was slightly smaller than one before, reaching the polymer surface roughness limit around Ra = 71.27 nm, which was decided by the nature of the polymer itself. This study proposed the references for the design and fabrication of mold cavities and parts, and saved time and cost in the actual product manufacturing.