Extrinsic contrast agents with excellent light absorption properties in the second near-infrared (NIR-II, 1000-1350 nm) region can be a key to enhance the contrast of photoacoustic imaging (PAI) in deep tissues. Here, we demonstrated a photoacoustic (PA) contrast agent at 1064 nm optical wavelength for deep-tissue in vivo PAI. We successfully synthesized nickel(II) dithiolene-based polymeric nanoparticles (NNP) that have strong absorption at NIR-II light and generate improved PA signal with a 1064 nm pulse laser. To confirm the feasibility of the NNP, we have conducted both in vitro and in vivo PA experiments and acquired highly contrast-enhanced PA images. We successfully obtained contrast-enhanced PA images of a tube filled with NNP deeply located below several layers of chicken tissue. The maximum PAI penetration depth was about 5 cm. Next, we performed bladder, sentinel lymph node and gastrointestinal tract, which are clinically important, PAI in rats to confirm that NNP could be utilized as a PA agent in deep tissues in vivo. NNP was injected into each of the three cases, and we confirmed that PA contrast was significantly increased after the injections. These results demonstrate that the enhanced PA signals generated by irradiating 1064 nm laser to NNP in deep-tissue has sufficient contrast for PAI. Based on the excellent absorbability of NNP at 1064 nm and the translability of clinical PAI systems, this study is expected to provide a great opportunity for a variety of studies on non-invasive deep tissue in vivo.