Coarse-grained molecular dynamics simulations were carried out to identify the conditions under which the nanorods (NRs) side-grafted with polymer chains can assemble in end-to-end configurations in a homopolymer matrix, a structure of significant importance for optimal property characteristics. Our results demonstrate that by adjusting the grafting density and the grafted chain length, three different NR morphologies can be obtained, viz., side-by-side aggregation, end-to-end alignment and homogeneous dispersion. To understand the underlying mechanism, the chain characteristics around the NRs were systematically investigated. We find that the transition of NR morphologies from side-by-side aggregation to others is correlated to the mushroom-to-brush transition of the grafted chain configurations. At high grafting densities corresponding to the brush regime, the entropic steric repulsions between the polymer brushes prevent the NRs from approaching in side-by-side configurations. Instead, end-to-end assembly and homogeneous dispersion are observed. Within such regimes, we observe that the splaying of the grafted polymer chains at the edges of the NRs plays a critical role in determining the occurrence of end-to-end assembly. When the extent of splaying cannot overcome the van der Waals and depletion attractions between the NR ends, which occurs at relatively short graft lengths, the end-to-end assembly is preferred. We find that this manner of self-assembly will be further promoted by increasing the NR loading but is retarded by increasing the NR aspect ratio. In general, our study identifies conditions to enable the end-to-end assembly of NRs in a homopolymer matrix, enabling significant practical applications.