The condensed states of biological macromolecules and their dynamic changes are related to many important physiological and pathological processes, such as coagulation and Alzheimer’s disease. Study of these processes is essential for patients with coagulation-associated diseases or Alzheimer’s disease. The development of effective regulating agents capable of interacting with such biomolecules has been suggested as a solution for diagnosis and therapy. The application of nanotechnology to medicine enable the design and fabrication of novel functional nanomaterials for disease treatment. In this review, we summarize the recent successful efforts to employ functional nanomaterials for regulating coagulation(triggering tumor vessel occlusion or fabricating nanoanticoagulants) and altering the aggregation and clearance of amyloid-β(Aβ). The remaining challenges and open opportunities are also discussed.