Malachite green (MG), a widely used antiparasitic agent, poses health risks to human due to its genotoxic and carcinogenic properties. Herein, a stable dual-emission fluoroprobe of carbon dots/copper nanoclusters is prepared for highly selective detection of MG based on the inner filter effect. This probe exhibits characteristic emission bands at 435 and 625 nm when excited at 376 nm. After adding MG, the both emission signals were significantly quenched, and the ratio of fluorescence intensity (F435/F625) was linearly related to the concentration of MG in the range of 0.05–40 μmol L−1 with a limit of detection of 18.2 nmol L−1. Meanwhile, the two signals exhibit linear relationships with the concentration of MG, respectively, and the corresponding detection results were consistent. The fluoroprobe was successfully used for the detection of MG in fish samples with the recoveries ranging from 96.0% to 103.8% and a relative standard deviation of <3.3%.