Ultrasound-based multimodal molecular imaging and functional ultrasound contrast agents (UCAs) have garnered great interest in biomedical imaging over the past few years. With the rapid development of molecular imaging technique, UCAs with singlefunction and single imaging modality can no longer satisfy increasingly growing medical diversification and hominization demand. The device of functional UCAs including multimodality and multifunction is of great value for disease diagnosis, treatment and research, and greatly accelerate the development of ultrasound-based multimodal molecular imaging. Functional UCAs can not only be applied for multimodality imaging to compensate for the disadvantages of each imaging modality whilst taking advantage of their individual strengths to acquire more biological information, but also can act as a vector carrying drugs or therapeutic genes to accomplish the combination of diagnosis and treatment, which is an existing study hotspot and has achieved initiatory success. In this paper, we reviewed the advances of ultrasound-based multimodal imaging, multimodal and multifunctional UCAs.