With more dynamic information available, researchers’ attention has recently shifted from static properties to dynamic properties of protein–protein interaction networks. To compensate the limited ability of technologies of detecting dynamic protein–protein interactions, dynamic protein interaction networks (DPINs) can be constructed by involving proteomic, genomic, and transcriptome analyses. Two groups of DPIN construction methods are classified based on the different focuses on dynamic information extracted from gene expression data. The dynamics of one kind of DPINs is reflected by the changes in protein presence varying with time, while that of the other kind of DPINs is reflected by the differences of coexpression under different conditions. In this review, the applications on DPINs will be discussed, including protein complexes/functional modules and network organization analysis, biomarkers detection in the progression or prognosis of the disease, and network medicine. We also point out the challenges in DPINs construction and future directions in the research of DPINs at the end of this review.