Compared to parametric counterparts, non-parametric (aka, model-free) damage detection methods have no requirements of accurate models, with the potential of autonomous monitoring of various complex structures. However, noises, or low signal-to-noise ratio (SNR), are one of the main challenges. This study is aimed at improving blind source separation (BSS)-based damage detection method, one of the most advanced non-parametric methods, in both aspects of noise robustness and autonomous operation. In particular, the measured acceleration responses are processed by variational mode decomposition (VMD) and wavelet transform (WT) in sequential, acting as the input for a BSS model. The BSS is then solved by independent component analysis (ICA), which approves to be more noise-robust compared to the state-of-the-art counterparts. Furthermore, shapelet transform is applied to extract the universal shape-based spike-like feature from the BSS model for training a support vector machine (SVM) model, applicable to different structures; it finally automates the sudden damage detection process and enables online monitoring. The effectiveness of the proposed method is illustrated by a numerical example and an experimental test, and demonstrated by a real-world seismic-excited structure. The results show that both single and multiple sudden damages can be automatically detected with high accuracy. Compared with the existing BSS methods, the proposed BSS method is more capable to detect small damages at relatively low SNR. In addition, the classification accuracy of SVM is also improved when shapelet-based feature is used for training, which reduces the malfunction of automated damage detection as shown by the numerical example. Therefore, the proposed strategy has the potential for rapid condition assessment of structures during rare/extreme events, before engineers are sent for further post-event inspection.