InAs/GaAs quantum dot (QD) is one of the promising material systems for the quantum information processing due to their atomic-like optical and electrical properties. There are many previous researches reporting the InAs QDs which can be implemented as solid-state single-photon sources for quantum information and quantum computing. However, the site-controlled growth of QDs is the prerequisite for addressability and integration. There are very few researches focusing on the systematic study of preferential nucleation of InAs QDs on a patterned GaAs (001) substrate. In this work, we study the preferential nucleation sites of InAs QDs on a patterned GaAs (001) substrate with different trench sidewall inclinations. With small inclination angle of the trench sidewalls, the InAs QDs nucleate preferentially inside the trenches, while with large inclination angle, the edges of the trenches appear to be the preferential nucleation sites. By utilizing the established method, a pair of InAs dots can be uniformly achieved in the patterned pits through tuning the inclination angle of the pits. The site-controlled single InAs QD and InAs QD molecules on the patterned substrates could have potential applications in quantum information processing and quantum computing.