Predicting carbon emissions is important in various sectors, including environmental management, economic planning, and energy policy. Traditional forecasting models typically require extensive training data to achieve high accuracy. However, carbon emission data are usually available on an annual basis, which is insufficient for effectively training conventional forecasting models. To address this challenge, this paper introduces an innovative carbon emissions prediction model that integrates Fibonacci attenuation particle swarm optimization (FAPSO) with the gated recurrent unit (GRU). The FAPSO algorithm is used to optimize the hyperparameters of the GRU, thereby alleviating the decline in prediction accuracy that conventional recurrent neural networks often face when dealing with limited training data. To evaluate the effectiveness of the FAPSO-GRU model, we tested it using carbon emission data from Hainan Province. Compared to the conventional GRU model, the FAPSO-GRU model achieved a significant reduction in the mean absolute error (42.27%), root mean square error (42.38%), and mean absolute percentage error (43.06%). Furthermore, we validated the FAPSO-GRU model with real data from Beijing, Guangdong, Hubei, Hunan, and Shanghai. The experimental results convincingly demonstrate that the proposed model provides a highly accurate solution for carbon emission prediction tasks, effectively addressing the limitations posed by limited training data.