Adjuvant chemotherapy is a critical regime in cancer treatment. The magnetic targeted drug delivery system (MTDDS) can selectively aggregate chemotherapy agents at the target areas, which has attracted great attention due to its safety, high efficiency, and minimal side effects on the human body. It would be ideal to establish a tissue engineering scaffold that can not only reconstruct the defect from the surgical tumor removal, but also serve as a magnetic station to attract MTDDS to the local site to enhance the targeted drug delivery. The current study constructed polycaprolactone magnetic tissue engineering scaffolds with various micrometer-sized magnets. The degradation properties of the scaffolds were assessed in simulated body fluid (SBF), and primary mouse bone marrow stromal cells were used to evaluate the biocompatibility of the scaffolds to osteoblast differentiations. The scaffolds were further examined by implantation to an air pouch model on the back of BALB/c mice. The in vitro data suggested that up to 40% of micron-sized magnetite can be used to formulate porous polycaprolactone (PCL) scaffolds with comparable biocompatibility to the PCL-alone scaffold. A mouse study revealed that the intro-peritoneal injected fluorescence-magnetic particles were collectedly enriched in the mouse air pouch tissues containing the 20% magnetic/PCL scaffolds. Histological assessment and the real-time PCR results of the air pouches confirmed the benign biocompatibility of the implanted magnetic scaffolds. © 2025 by the authors.