The mud pump water sealing system (MPWSS) is important in the efficient operation and prolonged service life of the cutter suction dredger’s (CSD) mud pump. Considering that the underwater pump operates underwater and the shaft seal water pressure sensor is prone to failure, a hybrid deep learning model MCNN transformer is proposed to predict the underwater pump shaft seal water pressure in the event of sensor failure. This paper uses big data from the dredging project to deeply excavate the relationship between the shaft end sealing water pressure and other construction data by combining experience and artificial intelligence, and then uses multi-scale convolutional neural network (MCNN) to reconstruct the data, highlighting the time series characteristics of the multi-scale data were then input into the transformer model for prediction, and compared with a single MCNN, transformer model and four other neural networks. Finally, the cutter suction dredger “Hua An Long” was selected as an application research case; experimental comparisons were conducted on seven different models to verify the accuracy and applicability of the MCNN-transformer model.