Microcystin-leucine-arginine (MC-LR) produced by various cyanobacteria during harmful algal bloom poses serious threats to drinking water safety and human health. Conventional chromatography-based detection methods require expensive instruments and complicated sample pretreatment, limiting their application for on-site detection. Colorimetric aptasensors are simple and rapid, and are amenable to fast detection. However, they provide only one output signal, resulting in poor sensitivity and accuracy. Dual-channel ratiometric colorimetric method based on the peroxidase-like activity of nanozyme can achieve self-calibration by recording two reverse signals, providing significantly enhanced sensitivity and accuracy. CeO2 nanocages (CeO2 NCs) with tetra-enzyme mimetic activities (oxidase-, peroxidase-, catalase- and superoxide dismutase-like activities) were facilely synthesized using zeolitic imidazolate framework-67 (ZIF-67) as sacrificial template. The peroxidase-like activity of CeO2 NCs can be regulated by DNA, and it showed opposite response to two chromogenic substrates (2,2'-azino-bis-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) and 3,3',5,5'-tetramethylbenzidine (TMB)), which was mainly attributed to the changed affinity. On the basis of MC-LR aptamer-tunable peroxidase-like activity of CeO2 NCs in TMB and ABTS channel, a dual-channel ratiometric colorimetric aptasensor was constructed for detection of MC-LR. Compared with conventional single-signal colorimetric assays, the proposed method showed lower limit of detection (0.66 pg mL−1) and significantly enhanced sensitivity. Moreover, the practicability of the ratiometric colorimetric assay was demonstrated by detecting MC-LR in real water samples, and satisfactory recoveries (94.9-101.9%) and low relative standard deviations (1.6-6.3%) were obtained. This work presents a nanozyme-based ratiometric colorimetric aptasensor for MC-LR detection by recording the reverse responses of two chromogenic reactions. Benefiting from the self-calibration function, the method can achieve higher sensitivity and accuracy. The short detection time and practical application in real water samples show greating potential for environmental monitoring.