Mesenchymal stem cells (MSCs), exhibiting tumor-tropic and migratory potential, can serve as cellular carriers to improve the effectiveness of anticancer agents. However, several challenges, such as the safety issue, the limited drug loading, the conservation of stemness and migration of MSCs, still remain in the MSC-based delivery system. In the present study, a novel nano-engineered MSC delivery system was established by loading doxorubicin (DOX)-polymer conjugates for the systemic treatment of pulmonary metastasis of breast cancer. For the first time, a dual drug-loaded mode, endocytosis and membrane-bound, was adopted to achieve the maximum amount of DOX conjugates in MSCs. The in vitro studies revealed the loaded MSCs possessed multifunctional properties, including preservation of the stemness and migration of MSCs, excellent stability of drug loading, acid sensitive drug release and obvious cytotoxicity against 4T1 cells. The in vivo studies confirmed that the loaded MSCs mainly located and long stayed in the lung where the foci of metastatic tumor situated. Importantly, loaded MSCs can significantly inhibit the tumor growth and prolong the life span of tumor-bearing mice in contrast with DOX and DOX-conjugate. The present loaded MSCs system suggested a promising strategy to solve several issues existed in cell-based delivery systems. Especially for the problem of low drug loading, the strategy, simultaneously loading nanodrug in cells' internal and membrane, might be the most desirable method so far and could be developed as a generalizable manner for cell-mediated tumor-targeted therapy.