Exposure to air pollution will pose a serious threat to human health. Accurate air pollution forecasting can help people to reduce exposure risks and promote environmental pollution control, and it is also an extremely important part of smart city management. However, the current deep-learning-based models for air pollution forecasting usually focus on prediction accuracy improvement without considering the model interpretability. These models usually fail to explain the complex relationships between prediction targets and external factors (e.g., ozone concentration (O3), wind speed, temperature variation, etc.) The relationships between variables in air pollution time series prediction problems are very complex, with intricate relationships between different types of variables, often with nonlinear multivariate dependencies. To address these problems mentioned above, we proposed a hybrid autoformer network with a genetic algorithm optimization to predict air pollution temporal variation as well as establish interpretable relationships between pollutants and external variables. Furthermore, an elite variable voting operator was designed to better filter out more important external factors such as elite variables, so as to perform a more refined search for elite variables. Moreover, we designed an archive storage operator to reduce the effect of neural network model initialization on the search for external variables. Finally, we conducted comprehensive experiments on the Ma’anshan air pollution dataset to verify the proposed model, where the prediction accuracy was improved by 2–8%, and the selection of model influencing factors was more interpretable.