In recent years, targeted ultrasound contrast agents (UCA) have emerged with the rapid development of contrast-enhanced ultrasound technology and bio-nanotechnology, showing good prospects for applications in molecular imaging and targeted therapy. The non-invasive treatment modality can reduce the drug dosage, toxicity and side effects, providing a new kind of methodology and approach for treatments, which will greatly expand the research and its applications. Targeted UCA have been developed rapidly in recent years, and a variety of new UCA appear, such as multi-functional UCA, multi-modal UCA, UCA with double ligands or more ligands, long-circulating UCA and immune type UCA, which meet growing clinical and research needs. The novel UCA have made a great progress and play an increasingly important role in molecular imaging. In this article, we reviewed the concepts of ultrasound molecular imaging, and summarized the applications of targeted UCA in molecular imaging and targeted therapy.