Selecting high molecular weight has become a quite popular approach for effective tuning of more shish-kebabs in semi-crystalline polymers. However, here, an unusual dependence of shish-kebabs on molecular weight of high-density polyethylene (HDPE) is found under the injection molding with a secondary flow. Characterization with electron microscope and X-ray scattering of the crystal structures reveals that the richest shish-kebabs develop in the HDPE with medium high molecular weight (HMW) chains rather than in the HDPE with more HMW chains. Both macroscopic scales (fluid behaviors related to the intensity of flow) and molecular scales (rheological properties related to orientation and relaxation) need to be overall considered and a physical model has been proposed to explain how the coupling between the chain architectures and the secondary flow field contributes to the unusual phenomenon. The factors, such as molecular parameters, interfaces between dispersed phase, and matrix as well as the properties of filler, profoundly influence both the two scales, which can be employed to tune the morphology related to physical properties. These significant results provide a simple but effective morphology control technique under a secondary flow field.