Robot trajectory prediction is an essential part of building digital twin systems and ensuring the high-performance navigation of IoT mobile robots. In the study, a novel two-stage multi-objective multi-learner model is proposed for robot trajectory prediction. Five machine learning models are adopted as base learners, including autoregressive moving average, multi-layer perceptron, Elman neural network, deep echo state network, and long short-term memory. A non-dominated sorting genetic algorithm III is applied to automatically combine these base learners, generating an accurate and robust ensemble model. The proposed model is tested on several actual robot trajectory datasets and evaluated by several metrics. Moreover, different existing optimization algorithms are also applied to compare with the proposed model. The results demonstrate that the proposed model can achieve satisfactory accuracy and robustness for different datasets. It is suitable for the accurate prediction of robot trajectory.