Residual cancer stem-like cells (CSCs) can cause tumour recurrence within a narrow margin around the initial tumour resection lesion, increasing the risk of post-surgical relapse and incurability. Currently, there are no efficient strategies for tracking and eradicating CSCs. Here we propose a nanovaccine strategy, called NICER, based on a nanovesicle system integrating CSC-specific antigen display and epigenetic nano-regulator encapsulation with a dendritic-cell-targeting aptamer, to simultaneously eradicate CSCs and bulk tumour cells. Specifically, nanovesicles derived from aldehyde-dehydrogenase-overexpressing tumours could serve as integrated antigens carrying both CSC-specific antigen and tumour-associated antigen. Epigenetic nano-regulator targeting YTH N6-methyladenosine RNA binding protein 1 could restrict dendritic cell lysosomal protease activity to modulate the effective cross-presentation of integrated antigens via major histocompatibility complex class I for immune responses. Overall, NICER represents a broad-spectrum vaccine approach against both CSCs and bulk tumours that can significantly inhibit postoperative cancer recurrence and metastasis, prolonging survival rates.