The invention discloses a maize yield combined prediction system and method. The prediction system comprises a data input module, a model base and intelligent combined module, a combined prediction module, a parameter management module and a result check and output module. The prediction method includes the steps that yield prediction is divided into sown area prediction and per-unit-yield prediction, models are selected to be combined according to predicted targets, the weights of sub-models of the combined model are determined according to the basic data change amplitude, the combined prediction result is acquired according to weight distribution of the combined model and checked, and finally the combined prediction result is output through diagrams and characters. Different prediction models are correspondingly combined according to different prediction durations, prediction variable factors and prediction basic data, maize yield prediction is pertinently conducted, the prediction result is higher in accuracy, the application range is wider, short-period and medium-and-long-term dynamic prediction can be achieved at the same time, and agricultural research requirements are met.