In order to explore the erosion damage mechanism of polymer cement protective layer on concrete surface of water transfer project under the action of high-speed water flow, the erosion characteristics of protective layer were studied by using improved high-pressure water gun erosion test equipment. Four characteristic parameters including maximum length, maximum width, maximum depth, and volume of erosion area were extracted by 3D scanning. The erosion damage pattern, damage parameter evolution law, and damage mechanism of protective layer under different spray pressure, spray length, spray angle, and spray time were analyzed. Taking the maximum erosion depth of protective layer as the target value, a prediction model of protective layer erosion depth based on Logistic regression function was established. Results show that under the same working conditions, the four erosion damage characteristic parameters of protective layer all increased with the increase in spray pressure and erosion time. With the increase in spray length (from 0.5 cm to 6.6 cm), the erosion pattern of protective layer changed from "hourglass" to "strip". In this process, the damage effect of hydraulic fracturing on the interface between protective layer and concrete decreased. The proposed prediction model of erosion depth of protective layer achieved good accuracy, and the erosion damage degree of protective layer could be significantly reduced by increasing the spray length and spray angle, which provides a reference for the surface protection design of concrete engineering.