Magnetic nanomotors (MNMs), powered by a magnetic field, are ideal platforms to achieve versatile biomedical applications in a collective and spatiotemporal fashion. Although the programmable swarm of MNMs that mimics the highly ordered behaviors of living creatures has been extensively studied at the microscale, it is of vital importance to manipulate MNM swarms at the nanoscale for on-demand tasks at the cellular level. In this work, a Cy5-tagged caspase-3-specific peptide-modified MNM is designed, and the adaptive control behaviors of MNM swarms are revealed in lysosomes to induce the cancer cell apoptosis under a rotating magnetic field (RMF). A magneto-programmed vortex is predicted to occur with swarms under RMF by the finite element method model and verified . According to the dynamic model and numerical simulation, the critical rotating frequency under which MNMs are out of step is strongly correlated to their assembling and swarming properties. The adaptivity of swarms maximizes the synchronous rotation to achieve an optimal energy conversion rate. The frequency-adapted controllability of MNM swarms for cancer cell apoptosis is observed in real time and . This work provides theoretical and experimental insights to adaptively control MNM swarms for cancer treatment.