Despite the fact that engineered surface enabling remarkable phase change heat transfer have elicited increasing attention due to their ubiquitous applications in thermal management, the underlying mechanisms of intrinsic rough structures as well as the surface wettability on bubble dynamics remain to be explored. Therefore, a modified molecular dynamics simulation of nanoscale boiling was conducted in the present work to investigate bubble nucleation on rough nanostructured substrates with different liquid-solid interactions. Specifically, the initial stage of nucleate boiling was mainly investigated and the bubble dynamic behaviors were quantitively studied under different energy coefficients. Results shows that as the contact angle decreases, the nucleation rate increases, because liquid obtains more thermal energy there compared with that on less wetting surfaces. The rough profiles of the substrate can provide nanogrooves, which can enhance initial nucleate embryos, thereby improving thermal energy transfer efficiency. Moreover, atomic energies are calculated and adopted to explain how bubble nuclei are formed on various wetting substrates. The simulation results are expected to provide guidance towards surface design in state-of-the art thermal management systems, such as the surface wettability and the nanoscale surface patterns.