Rituximab, a monoclonal antibody against the CD20 molecule expressed on B cells, has revolutionized the treatment of B cell lymphomas. The use of rituximab significantly improves the long-term survival rates of lymphoma patients. However, there are still many patients who develop resistance to rituximab. Hence, the urgent need is enhancing the potency of anti-CD20 antibodies beyond that achieved with rituximab to provide effective therapies for more patients. Traditional studies about the killing mechanisms of rituximab are commonly based on optical microscopy, which cannot reveal the detailed situations due to the limit of 200-nm resolution. Quantitatively investigating the actions of rituximab at the nanoscale is still scarce. The advent of atomic force microscopy (AFM) provides a powerful and versatile platform for in situ investigating the nanoscale behaviors of individual live cells. The applications of AFM in life sciences in the past decade have yielded a lot of novel insights into cell biology and related diseases. In this article, the typical applications (e.g., ultra-microstructures, mechanical properties, and molecular recognition) of AFM in investigating the three killing mechanisms of rituximab at the nanoscale are summarized; the challenges facing AFM single-cell assay and its future directions are also discussed.