The engineering plastic nylon 11 (PA11) with a processing temperature close to polyoxymethylene (POM) was introduced to the POM/carbon nanotubes (CNTs) system to prepare POM/PA11/CNTs ternary composite. The morphology structure of the dispersed phases including PA11 and CNTs in the corresponding micro part and the conventional macropart samples, the crystallization melting behavior and the filling behavior under the different micro injection processing conditions were investigated. The SEM results show that in the conventional injection molded samples, the PA11 phases, which are present as many ellipsoidal particles, are irregularly distributed in the POM matrix resin. However, in the micropart, the distribution of PA11 phases shows multi hierarchy structural features. In the skin layer and the shear layer of the samples, there are many fibrillar structures of PA11 phases formed, which are orientated along the melt flow direction. In the core layer, the degrees of the fibrillation and also the orientation of PA11 phases obviously become weakened. In addition, whether for the micropart or the conventional macropart, most of the involved CNTs are either selectively dispersed in the PA11 dispersed phase. The DSC results show that the addition of PA11 restrict the POM crystallization. With increase in injection speed or mold temperature, the corresponding melting peak of POM equally shifts toward high temperature. Finally, the filling behavior of above ternary composite system in the micro cavity was also investigated by the on line measurement of the micro molding machine.