As a critical component for space exploration, navigation, and national defense, array antenna secures an indispensable position in national strategic significance. However, various parts and complex assembly processes make the array antenna hard to meet the assembly standard, which causes repeated rework and delay. To realize the accurate and efficient prediction of the assembly accuracy of array antenna, a prediction method based on an auto-encoder and online sequential kernel extreme learning machine with boosting (Boosting-OSKELM) is proposed in this paper. The method is mainly divided into two steps: Firstly, the auto-encoder with the fine-tuning trick is used for training and representation reduction of the data. Then, the data are taken as the input of Boosting-OSKELM to complete the initial training of the model. When new sample data is generated, Boosting-OSKELM can realize the online correction of the model through rapid iteration. Finally, the test shows that the average MSE of Boosting-OSKELM and ANN is 0.061 and 0.12, and the time consumption is 0.85 s and 15 s, respectively. It means that this method has strong robustness in prediction accuracy and online learning ability, which is conducive to the development of array antenna assembly.