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Microwave propagation is adversely affected by evaporation duct, which can occur as often as 85% of the time in the sea of the world. Evaporation duct propagation is the abnormal bending and diversion of electromagnetic radiation from the intended paths, that resulting in the problems of extended propagation of microwave signals well beyond the radio horizon, high probability of intercept, measurement errors, radar holes, and anomalous clutter. A kind of anomalous clutter caused by evaporation duct propagation is described through analysis of experimental data collected from an S-band search radar. To suppress the anomalous clutter, a MTI processing with entropy detection is proposed, which utilizes the weak correlation characteristic and the certain position relation between anomalous clutter echoes. Compared with normal MTI processing, it can suppress anomalous clutter effectively and the performance is validated by simulation of the experimental data.