Metal-polymer hybrids are widely used due to large demands of lightweight materials. Pretreated metal was proved to join with polymer through injection molded direct joining (IMDJ). Many experimental results indicate that polymer infiltration into metal surface textures results in the joining. However, the detail joining mechanism has not been clarified, especially when surface structures are in nanoscale. Generally, nanostructures are suitable for mass production of small parts. Thus, for its further application, we aimed to study the effect of nanostructure size on the polymer infiltration and joining strength to clarify the joining mechanism. About surface nanostructures, we anodized metal (aluminum) pieces in different voltages for different pore intervals and etched it to control the pore diameter and porosity. Nano-porous structures with different sizes (diameter in 70, 200, 400, 600 nm) were fabricated on metal surface. We used these four kinds of metal pieces for IMDJ at different injection speeds. The joining strength was evaluated by tensile test and the negative dependence of joining strength on the injection speed with all of the structure sizes was confirmed. The polymer infiltration under various injection speeds were also investigated by atomic force microscopy after dissolving metal parts of joint specimens. The negative dependence of polymer replication on the injection speed is confirmed when the structure size is smaller than 200 nm while the positive dependence when larger than 400 nm. It is considered that the length of polymer molecular chain is about 300 nm, and the high speed can make the chain orient well so that it became difficult to replicate into small structures. In addition, we found that total replicated areas reduced according to the improvement of injection speed, which was mainly responsible for the negative dependence of joining strength on the injection speed especially for large structures.