Cancer cells are a class of important tumor biomarkers and are closely related to tumorous progression. It is urgent to develop a sensitive and highly efficient method for the rapid and accurate detection of cancer cells. Herein, an aptamer sandwiched nanochannel electrochemical sensor was established for the highly selective determination of cancer cells. By virtue of the porous nanochannels as the filter platform and immobilized with DNA aptamers for specifically capturing the cancer cells, the nanochannel‐based electrochemical sensor denotes excellent performance for MCF‐7 screening, and allowing a low limit of detection of 36 cells mL−1. The nanochannels‐based sandwich structure aptasensor not only presents an efficacious and reliable approach for cancer cell detection but also provides great advantage for preventing electrode passivation in the process of biomarkers analysis. An aptamer sandwiched nanochannel electrochemical sensor was constructed for the highly selective determination of cancer cells. The structure design of nanochannel composite aptasensor not only presents an efficacious and reliable approach for cancer cell detection but also provides advantage for preventing electrode passivation in the process of biomarkers analysis.