Research on controlling wrinkles of stiff thin films on soft substrates is important for developing low-cost methods for creating micro-structures on a surface. In this paper, dip-coating with an acetonitrile solution of poly(methyl methacrylate) on a UV–ozone-treated poly(dimethylsiloxane) substrate was investigated. After the dip-coating and subsequent drying process, wrinkles were observed on the surface. Although one of the origins of the wrinkling was the swelling of the substrate surface with acetonitrile, the alignment of the wrinkles was successfully controlled by wrapping the substrate around a pipe during the dip-coating. The other origin was mechanical compressive stress in the coating, which was induced when the substrate was released from the pipe. Due to these origins, the wrinkles were aligned in two directions crossing each other at right angles, and a well-ordered checkerboard pattern was formed. The size of a unit cell of such a checkerboard pattern was typically 86 μm wide, 142 μm long, and 10 μm deep. Because the dip-coating method does not require any vacuum processes, it is potentially advantageous for wrinkling a large surface using a continuous production process.