The flourish of the Internet of Things (IoT) and data-driven techniques provide new ideas for enhancing agricultural production, where evapotranspiration estimation is a crucial issue in crop irrigation systems. However, tremendous and unsynchronized data from agricultural cyber-physical systems bring large computational costs as well as complicate performing conventional machine learning methods. To precisely estimate evapotranspiration with acceptable computational costs under the background of IoT, we combine time granulation computing techniques and gradient boosting decision tree (GBDT) with Bayesian optimization (BO) to propose a hybrid machine learning approach. In the combination, a fuzzy granulation method and a time calibration technique are introduced to break voluminous and unsynchronized data into small-scale and synchronized granules with high representativeness. Subsequently, GBDT is implemented to predict evapotranspiration, and BO is utilized to find the optimal hyperparameter values from the reduced granules. IoT data from Xi'an Fruit Technology Promotion Center in Shaanxi Province, China, verify that the proposed granular-GBDT-BO is effective for cherry tree evapotranspiration estimation with reduced computational time, and acceptable and robust predictive accuracy. Consequently, the precise estimation of crop evapotranspiration could provide operational guidance for plant irrigation, plant conservations, and pest control in the agricultural greenhouse.