To investigate the effects of breathing cracks on the dynamic characteristics, i.e., natural frequencies, vibration displacement, slope angle, and bending moment, of a drilling riser, a time-domain finite element method based on the fracture mechanics theory is developed. The correctness of the proposed method is verified, and the performance of the different dynamic characteristics for crack identification is evaluated. First, the influence of the breathing and open cracks on natural frequencies is explored. The maximum frequency shifts vs crack location and water depth are studied. The results of the small difference of natural frequencies between intact and cracked risers illustrate that the traditional frequency-based crack-detection method is not applicable for the risers. Second, the time-domain motions, orbit plots, Poincaré maps, and fast Fourier transform diagrams are extracted for discussing the effects of the breathing and open cracks and crack depth and location. Finally, the second and fourth derivatives of the root-of-mean-square (RMS) of the dynamic response characteristics are defined for crack identification. It is found that the moment RMS has a good performance in single- and multiple-crack identifications and that not only locations but also degrees of the breathing cracks can be well detected by the proposed indices. In short, several conclusions drawn are a benefit for the safety of a serviced drilling riser system.