Risers are the conduits between the subsea wellhead and the drilling/production platform for development, production, gas lift or water injection purposes, which are also one of the most important and the most vulnerable components for deepwater floating platforms. To address the lack of appropriate global structural health monitoring (SHM) system for deepwater risers, this paper proposes a time-frequency domain approach using a wavelet modified second order blind identification (WMSOBI) method and combined distributed force change (CDFC) index. WMSOBI provides a reliable time-frequency domain identified modal properties of riser systems, even with large damping and under-determinate conditions. In addition, CDFC index generated from modal properties extracted by WMSOBI can accurately identify the damage location and damage level for both single and multiple crack scenarios. Details of experiments conducted on suspended pipe are presented. Both numerical and experimental verification are presented to validate the effectiveness of the proposed WMSOBI/CFDC algorithm and SHM system.