Crop evapotranspiration (ETC) is an important component of the agricultural hydrological cycle, and its accurate estimation is important for assessing the hydrological environment of farmlands and guiding crop irrigation. To improve the prediction accuracy of ETC for early and late rice, this study analyzed the importance of the influencing factors based on a categorical regression tree (CART) machine learning algorithm. Based on the importance results of the influencing factors obtained from CART analysis, different combinations of input factors were constructed, and daily ETC prediction models were developed for early and late rice using the least squares support vector machine (LSSVM). A three-element heuristic optimization algorithm, Sine Cosine Algorithm (SCA), Slime Mold Algorithm (SMA), and Sparrow Search Algorithm (SSA), were used to optimize the ETC model to improve the performance of the early and late rice ETC prediction models. The results of this study revealed that the strongest correlation between early and late rice ETC was net solar radiation (Rn), with importance of 0.830 and 0.802, respectively. The next strongest correlations were temperature (T), wind speed (u), soil moisture (SM) and u, leaf area index (LAI), SM (0.092, 0.02, 0.014 and 0.058, 0.049, 0.034), respectively. The accuracy of the model tended to increase as the number of influencing factors in the input combinations constructed based on the importance results increased. The accuracy of the model increased more rapidly when the input factors were one to four and the accuracy of the model increased slightly when the input factors were more than four. The SSA-LSSVM model with four-factor combinations of inputs was the least-factor combination with guaranteed model accuracy of RMSE = 0.514 mm/d, R2 = 0.924, KGE = 0.565, WI = 0.978,and MAE = 0.414 mm/d; RMSE = 0.468 mm/d, R2 = 0.910, KGE = 0.670, WI = 0.985, and MAE = 0.368 mm/d. This study may provide a reference for the prediction of evapotranspiration as a key factor in the study of the agricultural hydrological environment of early and late rice.