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Water stress is a significant element impacting photosynthesis, which is one of the major physiological activities governing crop growth and development. In this study, the photosynthetic rate of Brassica chinensis L. var. parachinensis (Bailey) (referred to as Chinese Brassica hereafter) was predicted using the deep learning method. Five sets of Chinese Brassica were created, each with a different water stress gradient. Air temperature (Ta), relative humidity (RH), canopy temperature (Tc), transpiration rate (Tr), photosynthetic rate (Pn), and photosynthetically available radiation (PAR) were measured in different growth stages. The upper limit and lower limit equations were built using the non-water-stress baseline (NWSB) and hierarchical density-based spatial clustering of applications with noise (HDBSCAN) methods. The crop water stress index (CWSI) was then calculated using these built equations. The multivariate long short-term memory (MLSTM) model was proposed to predict Pn based on CWSI and other parameters. At the same time, the support vector regression (SVR) method was applied to provide a comparison to the MSLTM model. The results show that water stress had an important effect on the growth of Chinese Brassica. The more serious the water stress, the lower the growth range (GR). The HDBSCAN method had a lower root mean square error (RMSE) in calculating CWSI. Furthermore, the CWSI had a significant effect on predicting Pn. The regression fitting between measured Pn and predicted Pn showed that the determination coefficient (R2) and RMSE were 0.899 and 0.108 μmol·m−2·s−1, respectively. In this study, we successfully developed a method for the reliable prediction of Pn in Chinese Brassica, which can serve as a useful reference for application in water saving. [ABSTRACT FROM AUTHOR]