The spatial presentation and concentration of surface function is often crucial for successful material function design. For the surface mimic and function studies, self-assembled monolayers (SAMs), that have easily tunable functions and wide variety of suitable reaction chemistries, provide a suitable strategy. Furthermore, combined with high-throughput combinatorial strategies, SAMs gradient surfaces, which can surveying a wide range of materials parameters in limited experimental trials and short time, enable the rapid, efficient and precise investigation of surface properties. In our study, we designed a novel “vacuum away” confined channel vapor deposition method, which is simple and easily controllable, and linear gradient chemical concentration profiles with tunable chemical functionalities were generated on silicon and glass substrates. In addition, two-dimensional (2D) orthogonal chemical concentration gradients were achieved by using a sequential deposition protocol which enables the orthogonal engineering of functional SAMs.