A hybrid algorithm (IWOA-BP) combining the improved whale optimization algorithm (IWOA) and backpropagation neural network (BP) was proposed to offer theoretical support for the formulation of grain strategies in the agriculture sector and its related industries. By introducing an improved convergence factor, nonlinear inertia weight, and optimal neighborhood disturbance strategy into the modified whale optimization algorithm, the optimal solution of the algorithm was obtained. This solution was then utilized as the initial weights and thresholds of the BP neural network, thereby enhancing the convergence speed and accuracy of the IWOA-BP hybrid algorithm. Subsequently, a grain yield prediction model based on the improved whale optimization algorithm was established using data from China’s grain yield over 45 years and seven influencing factors including effective irrigation area, chemical fertilizer application, rural electricity consumption, total power of agricultural machinery, sowing area of grain crops, disaster-affected area, and per capita consumption expenditure in rural areas. Through extensive experiments on a test set, it was found that the IWOA-BP model consistently outperformed other prediction models such as long short-term memory (LSTM), extreme learning machine (ELM), BP neural network with whale optimization algorithm (WOA-BP), and BP neural network with particle swarm optimization (PSO-BP). Compared to the ELM model, the root mean square error (RMSE) and mean absolute percentage error (MAPE) of the IWOA-BP model were reduced by 77.12% and 88.18% respectively. When compared to the LSTM model, the RMSE and MAPE of the IWOA-BP model were reduced by 69.11% and 47.36% respectively. Furthermore, in comparison to the WOA-BP model, the mean absolute error (MAE), RMSE, and MAPE of the IWOA-BP model were reduced by 43.78%, 43.22% and 45.96% respectively. Additionally, when compared to the PSO-BP model, the MAE, RMSE, and MAPE of the IWOA-BP model were reduced by 89.67%, 90.61% and 90.82% respectively. Therefore, the proposed IWOA-BP prediction model can be effectively used to predict grain yield due to its higher coefficient of determination, smaller prediction error, and faster convergence speed. It has important technical reference value for agricultural departments and relevant policymakers.