Achievement of a robust structural health monitoring (SHM) system for on-orbit composite boom structures requires development of proper structural models and accurate interpretation of sensor response are of great importance. In this paper, an integrated approach which includes multiscale modeling, Lamb wave analysis, and vibration based modal analysis is proposed to detect microscale matrix cracking in boom structures that are subjected to a flattening and wrapping process around a circular hub. Multiscale modeling of the booms provides a theoretical estimation of the material properties at different length scales, which becomes the reference for Lamb wave and modal analysis. The Lamb wave based active sensing technique proposed in this study is used to detect signal changes due to structural degradation with the aid of Matching Pursuit Decomposition (MPD) as a damage feature extraction tool. Vibration based modal analysis provides new damage features by correlating composite material degradation with modal frequency shifts. The comparison of different SHM methods confirms the effectiveness of the proposed integrated SHM approach. The proposed methodologies have been validated experimentally.