The mechanical performance of nanomaterials reinforced polymer nanocomposites is a pre-requisite for their engineering implementations, which is largely determined by the interfacial load transfer efficiency. This work investigates the role of the nanofillers via molecular dynamics simulations under different deformation scenarios, mimicking a maximum and minimum load transfer scenario from the polymer matrix. Based on the polyethylene (PE) nanocomposite reinforced by a new nanofiller – carbon nanothread (NTH), we find that the loading conditions dominantly determine its enhancement effect on the mechanical properties of the PE nanocomposite. Under tensile deformation, the ultimate tensile strength of the PE nanocomposite receives around 61% to 211% increment when the filler deforms simultaneously with the PE matrix. However, such enhancement is largely suppressed when the NTH is deforming non-simultaneously. Similar results are observed from the compressive deformation. Specifically, both morphology and functionalization are found to alter the enhancement effect from the NTH fillers, while also relies on the loading directions. Overall, this work provides an in-depth understanding of the role of the nanofiller. The observations signify the importance of establishing effective load transfer at the interface, which could benefit the design and fabrication of high-performance polymer nanocomposites.