We report the growth of GaN epitaxial layer on Si(001) substrate with nano-patterns prepared by dry etching facility used in integrated circuit (IC) industry. It was found that the GaN epitaxial layer prepared on nano-patterned Si(001) substrate exhibits both cubic and hexagonal phases. It was also found that threading dislocation observed from GaN prepared on nano-patterned Si(001) substrate was significantly smaller than that prepared on conventional unpatterned Si(111) substrate. Furthermore, it was found that we can reduce the tensile stress in GaN epitaxial layer by about 78% using the nano-patterned Si(001) substrate.