Circulating tumor cells (CTCs) are regarded as promising biomarkers for early clinical diagnosis, prognosis evaluation, and treatment monitoring. However, their limited abundance in peripheral blood and phenotypic heterogeneity resulting from epithelial-mesenchymal transition (EMT) present significant challenges for accurate detection of CTCs. Herein, we developed an ultrasensitive and highly specific cytosensor to address these limitations. Firstly, to overcome the EMT property of CTCs, we designed a novel 3D multivalent aptamer recognition strategy (MARS), which not only contributed to highly efficient capture of heterogeneous CTCs, but also guaranteed detection sensitivity of the developed cytosensor. Meanwhile, we integrated an exonuclease III (Exo III)-mediated DNA walking signal amplification strategy into the electrochemiluminescence (ECL) cytosensor, enhancing its sensitivity in detecting rare CTCs. Furthermore, in combination with the excellent ECL performance of the luminescent nanomaterials (Au@COF-LZU1@Ru), the cytosensor exhibited a wide detection range from 8 to 1 × 105 cells/mL with a detection limit as low as 2 cells/mL. The analytical performance of the constructed cytosensor was validated through real sample analysis (AUC = 0.97), demonstrating its potential for clinical applications. The novel cytosensor offers an effective and reliable tool for the detection of rare CTCs, thereby paving the way for improved clinical significance.