The precise transplantation, long-term tracking, and maintenance of stem cells with maximizing therapeutic effect are significant challenges in stem cell-based therapy for stroke treatment. In this study, a unique core-shell labeling nanoagent was prepared by encapsulating a cobalt protoporphyrin IX (CoPP)-loaded mesoporous silica nanoparticle (CPMSN) into a 125I-conjugated/spermine-modified dextran polymer (125I-SD) by microfluidics for mesenchymal stem cell (MSC) tracking and activity maintenance. The CPMSN core not only exhibits excellent photoacoustic (PA) imaging performance induced by the intermolecular aggregation of CoPP within the mesopores but also protects the MSCs against oxidative stress by sustained release of CoPP. Meanwhile, the addition of a 125I-SD shell can increase the uptake efficiency in MSCs without inducing cell variability and enable the single-photon-emission computed tomography (SPECT) nuclear imaging. In vivo results indicated that CPMSN@125I-SD labeling could allow for an optimal combination of instant imaging of MSCs, with PA to guide intracerebral injection, followed by multiple time point SPECT imaging to consecutively track the cell homing. Importantly, the sustained release of CoPP from CPMSN@125I-SD significantly increased the survival of MSCs after injection into an ischemic mouse brain and promoted neurobehavioral recovery in ischemic mice. Thus, CPMSN@125I-SD represents a robust theranostic probe for both MSC tracking and maintaining their therapeutic effect in the treatment of brain ischemia.