A method to prepare nanostructures based on injection molding was proposed by taking Anodic Aluminum Oxide (AAO) templates as the mold inserts. Mold temperatures, hydrophobic properties and service life of the mold inserts were studied. Firstly, the replication quality of the nanostructures under different mold temperatures was studied by comparing the morphologies and aspect ratios of three different AAO templates. Then, according to the hydrophobic property of a nano-array structure, the influences of structural characteristics and mold temperatures on the static contact angle were analyzed to explore the hydrophobicity in different regions of PC products. Finally, the macro/micro quality and service life of AAO templates were analyzed after injection molding process. The results indicate that the mold temperatures significantly affect the replication quality of nanostructures, which focuses on the molding heights of nanostructures. There are slight hydrophobic differences at different regions of injection molded parts. Compared to the PC products without nanostructures, the maximum contact angle increases by 31.5%, reaching to 108.2°. After 500 molding cycles or more, the AAO templates with low aspect ratios show good quality, while the defects in high aspect ratio AAO templates are quite obvious.