Nanomedicine involves the use of engineered nanoscale materials in an extensive range of diagnostic and therapeutic applications and can be applied to the treatment of many diseases. Despite the rapid progress and tremendous potential of nanomedicine in the past decades, the clinical translational process is still quite slow, owing to the difficulty in understanding, evaluating, and predicting nanomaterial behaviors within the complex environment of human beings. Microfluidics-based organ-on-a-chip (Organ Chip) techniques offer a promising way to resolve these challenges. Sophisticatedly designed Organ Chip enable in vitro simulation of the in vivo microenvironments, thus providing robust platforms for evaluating nanomedicine. Herein, we review recent developments and achievements in Organ Chip models for nanomedicine evaluations, categorized into seven broad sections based on the target organ systems: respiratory, digestive, lymphatic, excretory, nervous, and vascular, as well as coverage on applications relating to cancer. We conclude by providing our perspectives on the challenges and potential future directions for applications of Organ Chip in nanomedicine.