The poor central nervous system leukemia (CNSL) clinical efficacy of conventional doses of chemotherapy is mainly attributed to the limited permeability of chemotherapy agents caused by the blood-brain barrier (BBB). Effectively enhancing the accumulation of drugs across the BBB in the central nervous system is one of the key challenges in improving patient compliance and clinical efficacy of CNSL. Here, we find that the VP1 protein, the functional module of the John Cunningham (JC) virus, can safely penetrate the BBB through a sialic acid receptor-mediated transcytosis mechanism. Based on this, we develop a JC virus-mimicking nanodrug delivery platform based on VP1 protein-conjugated self-assembled nanoparticles (MFHV), which can active target and cross the BBB via a receptor-mediated transcytosis for safe and effective low-dose chemotherapy against CNSL after systemic administration. The results demonstrate that such a platform can penetrate the BBB through the dual mechanism of clathrin-mediated endocytosis and micropinocytosis pathway. When further synergistic with ferroptosis and histamine metabolism, the long-term survivors of low-dose MTX are significantly enhanced by 83.3 % and 56.7 % in two CNSL mice models. Collectively, this study takes a new perspective on natural living materials and molecule targeting of the BBB to present a promising strategy for low-dose chemotherapy against CNSL with safety and efficacy, which might provide a clinically translatable option for the prevention and treatment of CNSL.