This paper reviews the development and application of HHT in the field of SHM in the last two decades. The challenges and future trends in the development of HHT based techniques for the SHM of civil engineering structures are also put forward. It also reviews the basic principle of the HHT method, which contains the extraction of the intrinsic mode function (IMF), mechanism of the EMD, and the features of HT; shows the application of HHT in the system identification, which contains the introduction of theoretical method, the identification of modal parameters, and the system identification on real structures; and discusses the structural damage detection using HHT based approaches, which includes the detection of common damage events, sudden damage events, and cracks and flaws.