The morphologies of micro-injection molded parts are influenced by the process parameters. In this paper, the influence of injection speed, mold temperature and melt temperature on the morphologies of micro-injection molded polyformaldehyde (POM) parts with different thicknesses were investigated by a single factor experimental method; the morphological structure of the parts was characterized by polarized light microscopy. The scale effect on the crystallization behavior and internal morphology of micro-injection POM pans was analyzed. The results indicated that the scale effect had a great influence on the hierarchical morphology in the thickness direction of the parts. The micro-parts with a thickness of 1.0 mm showed a skin-core structure including the skin layer, fine grain layer, oblate spherulite, and spherulite core layer, and the micro-parts with a thickness of 0.2 mm showed a skin-core structure with the skin layer, fine grain layer, and the spherulite core layer, and a larger thickness ratio of the spherulite core layer. As injection speed, mold temperature and melt temperature increase, the fine grain layer gradually disappears and the size of core spherulite tends to become larger, the thicknesses of the skin layer of all the micro-parts decrease and that of the 0.2 nm micro-parts decreases significantly.