Herein, a multifunctional dual-modal imaging probe is successfully developed to integrate the advantages of second near-infrared window (NIR-II, 1000–1700 nm) fluorescence imaging (FI) and photoacoustic imaging (PAI) with the ultimate goal of improving diseases diagnosis and management. Melanin-inspired polydopamine (PDA) polymer coated NaYF4:Yb3+,Er3+@NaYbF4@NaYF4:Nd3+ down conversion nanoparticles (DCNPs) is designed via water-in-oil microemulsion method, which comprises a DCNP core, acting as the NIR-II optical imaging agent, and a PDA shell, acting as the PA contrast agent. By taking the advantages of high spatial resolution and excellent temporal resolution, the dual-modal contrast agent is capable for high sensitivity real-time visualization of gastrointestinal tract, diagnosis of gastrointestinal peristalsis disorder and NIR-II FI-guided intestinal obstruction surgery. All of the above results demonstrate the great potential of DCNP@PDA NP as an efficient NIR-II/PAI dual-modal contrast agent for precision medicine.