We report a methylene blue (MB)-modified electrochemical aptamer (E-AB) sensor for determining microcystin-LR (MC-LR). The signal transduction of the sensor was based on changes in conformation and position of MB induced by the binding between MC-LR and the modified aptamer probe. In the absence of MC-LR, an aptamer probe was considered partially folded. After combining aptamer and MC-LR, the configuration of the aptamer probe changed and facilitated the electron transfer between MB and the electrode surface. As a result, an increased current response was observed. We optimized the parameters and evaluated the electrochemical performance of the sensor using square wave voltammetry (SWV). MC-LR was measured from 1.0 to 750.0 ng/L with a detection limit of 0.53 ng/L. The reliability of the method was verified by the determination of MC-LR in environmental real samples, such as pond water and tap water. Moreover, we demonstrated that this reagent-less biosensor could be regenerated and reused after rinsing with deionized water with good accuracy and reproducibility. As a reusable and regenerable E-AB sensor, this rapid, reagent-free, and sensitive sensing platform will facilitate routine monitoring of MC-LR in actual samples.