A magnetically targeted drug delivery system (DDS) is developed to solve the delivery problem of hydrophobic drugs by using hollow mesoporous ferrite nanoparticles (HMFNs). The HMFNs are synthesized by a one-pot hydrothermal method based on the Ostwald ripening process. The biocompatibility of the synthesized HMFNs was determined by MTT assay, lactate dehydrogenase (LDH) leakage assay and hemolyticity against rabbit red blood cells. Moreover, Prussian blue staining and bio-TEM observations showed that the cell uptake of nanocarriers was in a dose and time-dependent manner, and the nanoparticles accumulate mostly in the cytoplasm. A typical highly hydrophobic anti-tuberculosis drug, rifampin (RFP) was loaded into HMFNs using supercritical carbon dioxide (SC-CO) impregnation, and the drug loading amount reached as high as 18.25 wt%. In addition, HMFNs could co-encapsulate and co-deliver hydrophobic (RFP) and hydrophilic (isoniazide, INH) drugs simultaneously. The release tests demonstrated extra sustained co-release profiles of rifampicin and isoniazide from HMFNs. Based on this novel design strategy, the co-delivery of drugs in the same carrier enables a drug delivery system with efficient enhanced chemotherapeutic effect.