Similar to mechanical forces that can induce profound biological effects, magnetic fields can have a broad range of implications to biological systems, from magnetoreception that allows an organism to detect a magnetic field to perceive direction, altitude, or location, to the use of heating induced by magnetic field for altering neuron activity. This review focuses on the application of magnetic forces generated by magnetic iron oxide nanoparticles (MIONs), which can also provide imaging contrast and mechanical/thermal energy in response to an external magnetic field, a special feature that distinguishes MIONs from other nanomaterials. The magnetic properties of MIONs offer unique opportunities for enabling control of biological processes under different magnetic fields. Here, we describe the approaches of utilizing the forces generated by MIONs under an applied magnetic field to control biological processes and functions, including the targeting of drug molecules to a specific tissue, increasing the vessel permeability for improving drug delivery, and activating a particular viral vector for spatial control of genome editing in vivo. The opportunities of using nanomagnets for a broad range of biomedical applications are briefly discussed.