A power generation prediction system using a first and second neural networks is provided, and the first neural network is connected to the second neural network. The first neural network receives first input data, and generates the amount prediction data according to the first input data. The first input data is used to determine amount prediction data, and the amount prediction data is used to determine power generation prediction data. The second neural network receives the amount prediction data, and calculates the power generation prediction data according to the amount prediction data. When a device in a selected area is deteriorated or reinstalled, the second neural network is fine-tuned and trained again. The power generation prediction data is a power generation prediction bound having a maximum and minimum power generation prediction values, and thus the power deployment terminal in a power grid can deploy power more precisely.