Objective To prepare multifunctional nanoparticles targeting thrombus, and to explore the physico-chemical properties, targeting effect, photoacoustic imaging ability and thrombolytic effect of the nanoparticles. Methods cCGPRPPC-DiR-PFP-PLGA nanoparticles (TNP) were prepared by double emulsification method and modified by carbodiimide technique, with poly(lactic-co-glycolic acid) (PLGA)，near-infrared fluorescent iodide (1,1’-dioctadecyl-3,3,3’,3’-tetramethylindotricarbocyanine iodide, DiR), perfluoropentane (PFP) and cCGPRPPC cyclic peptide. The morphology, particle size, zeta potential and polydispersity were observed by optical microscope and laser particle size analyzer; the encapsulation rate of DiR was detected by ultraviolet spectrophotometer; the conjugation of cyclic peptide with nanoparticles was detected by confocal microscopy and flow cytometry; the targeting properties of TNP were observed by confocal microscopy and fluorescence microscopy; the imaging ability of TNP was analyzed by photoacoustic imaging experiments; and TNP were used for thrombolysis in vitro and in vivo with low-intensity focused ultrasound (LIFU) irradiation. Results The particle was round, the size of TNP was (262.67±23.46) nm, the zeta potential was (－1.97±0.68) mV, the polydispersity index was 0.06±0.05, the DiR encapsulation rate was (82.00±0.03)%, and the conjugation rate of peptide with nanoparticles was (99.58±0.47)%. The photoacoustic signal intensity of TNP in vitro was concentration dependent. TNP could target thrombus both in vitro and in vivo. In vitro, the thrombolytic rate was (71.43±1.00)% at 30 min after LIFU irradiation. In vivo thrombolysis experiment, the photoacoustic signal intensity of thrombus decreased with the prolongation of LIFU irradiation time. Conclusion Thrombus targeting contrast agents, TNP, have been successfully prepared, which exhibiting photoacoustic imaging ability and thrombolytic effect in vitro and in vivo.