Optical-resolution photoacoustic microscopy (OR-PAM) is an imaging tool to provide in vivo optically sensitive images in biomedical research. To achieve a small size, fast imaging speed, wide scan range, and high signal-to-noise ratios (SNRs) in a water environment, we introduce a polydimethylsiloxane (PDMS)-based 2-axis scanner for a flexible and waterproof structure. The design, theoretical background, fabrication process and performance of the scanner are explained in details. The designed and fabricated scanner has dimensions of 15 × 15 × 15 mm along the X, Y and Z axes, respectively. The characteristics of the scanner are tested under DC and AC conditions. By pairing with electromagnetic forces, the maximum scanning angles in air and water are 18° and 13° along the X and Y axes, respectively. The measured resonance frequencies in air and water are 60 and 45 Hz along the X axis and 45 and 30 Hz along the Y axis, respectively. Finally, OR-PAM with high SNRs is demonstrated using the fabricated scanner, and the PA images of micro-patterned samples and microvasculatures of a mouse ear are successfully obtained with high-resolution and wide-field of view. OR-PAM equipped with the 2-axis PDMS based waterproof scanner has lateral and axial resolutions of 3.6 μm and 26 μm, respectively. This compact OR-PAM system could potentially and widely be used in preclinical and clinical applications.