Recently developed atmospheric pressure plasma jet (APPJ) is considered as a novel and efficient technique for uneven surfaces processing and APPJ array effectively expands the treatment area of a single APPJ. In this paper, a two-dimensional (2D) APPJ array in Ar/tetramethylsilane (TMS) is used to improve the surface hydrophobicity of polymethyl methacrylate (PMMA) by depositing polymerized silicalike clusters on the jet-PMMA interface. The electrical and optical characteristics of the 2D Ar/TMS APPJ array are measured to optimize experimental conditions. The wettability of jet-PMMA interface is assessed by measuring water contact angle, which increases from 65° to a maximum value of 115° after 240 s plasma treatment at 0.04% TMS content. Scanning electron microscopy is used to investigate the micro- and nanoscale surface morphology of PMMA after plasma treatment, and it is found that there are clusters of particles with diameters of hundreds of nanometers attached on the PMMA surface. The changes of the chemical composition and chemical bonding on the PMMA surface are further analyzed using Fourier transform infrared and x-ray photoelectron spectroscopies. It is found that the silicon-containing groups, such as Si-CH3, Si-H, and Si-O-Si, replace oxygen-containing hydrophilic polar groups (C—O and C=O), reduce the surface polarity, decrease the surface tension, and increase the surface hydrophobicity. For the intensive peak of Si-O-Si in FTIR spectra, the improvement of hydrophobicity of the PMMA surface is caused by the hydrophobic polymerized Si-O-Si thin film. The results demonstrate that the APPJ array as a novel atmospheric pressure plasma device provides an efficient way to modify large uneven material surfaces.