Smart agricultural sensing has enabled great advantages in practical applications recently, making it one of the most important and valuable systems. For outdoor plantation farms, the prediction of climate data, such as temperature, wind speed, and humidity, enables the planning and control of agricultural production to improve the yield and quality of crops. However, it is not easy to accurately predict climate trends because the sensing data are complex, nonlinear, and contain multiple components. This study proposes a hybrid deep learning predictor, in which an empirical mode decomposition (EMD) method is used to decompose the climate data into fixed component groups with different frequency characteristics, then a gated recurrent unit (GRU) network is trained for each group as the sub-predictor, and finally the results from the GRU are added to obtain the prediction result. Experiments based on climate data from an agricultural Internet of Things (IoT) system verify the development of the proposed model. The prediction results show that the proposed predictor can obtain more accurate predictions of temperature, wind speed, and humidity data to meet the needs of precision agricultural production.