High speed thin wall injection molding is becoming more and more important due to the explosive growth of portable devices. During of which, the combined effect of high shear stress fields and fast cooling rate may facilitate generating special morphology of polymer blends, thus provides us opportunity to prepare functional materials. In this study, high speed thin wall injection molding is utilized to fabricate anisotropic electrical conductive polymer composites (ACPCs) consisting of polypropylene (PP) and carbon nanotubes (CNTs) filled polyethylene (PE). It is demonstrated that the CNTs are localized in PE phase due to the premixing procedure and better affinity to PE. Furthermore, an alternating multilayer structure with different polymer phases elongated as well as conductive network oriented parallel to flow direction is observed. The morphological study from the runner to the mold indicates that the dispersed phase is firstly deformed into discontinuous layer structure, and finally deformed into wide and regular continuous layers. The good viscosity match, low interfacial tension, short relaxation time and high shear rate are characterized as important issues controlling the formation of alternating multilayer structure. The anisotropic conductive behavior of these ACPCs, i.e. conductive in longitudinal (parallel to flow direction) and transverse (perpendicular to flow direction) direction but non-conductive in thickness direction, is contributed by the insulating PP layer which cuts off the conductive networks in the core layer. More importantly, much better electromagnetic interference (EMI) shielding ability is obtained for these ACPCs with alternating multilayer conductive networks comparing with the same polymer blends with isotropic conductive networks, despite of the fact that much lower resistivity is obtained for the later. This study has shed some light on a range of potential applications using alternating multi-layered structure.