The thermal conductivity of backfill materials directly affects the heat transfer efficiency between energy geo-structures and the surrounding stratum. Microbially induced carbonate precipitation (MICP) possesses great potential for improving the thermal conductivity of backfill materials. Magnetic iron oxide nanoparticles (i.e., nano-Fe3O4) have been proven to enhance bacterial biochemical activity by altering the permeability of bacterial biofilms, thus potentially improving the MICP process. It was supposed to enhance the thermal conductivity of backfill materials, allowing for applying energy geo-structures in arid environments. In this study, MICP in a solution environment was conducted to analyze bacterial urease activity and morphology of precipitation at varying nano-Fe3O4 contents. Additionally, sand columns treated with MICP and different nano-Fe3O4 contents were performed to obtain the thermal conductivity and unconfined compressive strength (UCS) through the transient plane source (TPS) method and uniaxial compression (UC) experiment. The mineral type, precipitation morphology, and microstructure were identified using scanning electron microscopy (SEM) and X-ray diffraction (XRD). The mechanism of the effect of nano-Fe3O4 on bacterial urease activity and thermal-mechanical behaviors was also discussed. The results indicated that the nano-Fe3O4 could enhance bacterial urease activity and promote vaterite precipitation in the solution environment. Conversely, when applied to MICP-treated sand, nano-Fe3O4 could facilitate calcite formation. Increasing the nano-Fe3O4 content showed a positive correlation with increased thermal conductivity and UCS. Specifically, the optimal values of thermal conductivity and UCS increased by 2.42 times and 2.39 times, respectively, compared to MICP-treated specimens without nano-Fe3O4. Microstructure analysis revealed that calcite precipitation at the particle contact served a dual function: cementing particles, thereby improving the mechanical strength and simultaneously acting as a "thermal bridge" to enhance the thermal conductivity. Furthermore, this study provides a new perspective on utilizing magnetized bacteria to reinforce specific locations within rocks and soils in the presence of an external magnetic field.