To date, as the different application fields, most VR-based training systems have been different. Therefore, we should take the characteristics of application field into consideration and adopt different evaluation methods when evaluate the user experience of these training systems. In this paper, we propose a method to evaluate the user experience of virtual astronauts training system. Also, we design an experiment based on the proposed method. The proposed method takes learning performance as one of the evaluation dimensions, also combines with other evaluation dimensions such as: presence, immersion, pleasure, satisfaction and fatigue to evaluation user experience of the System. We collect subjective and objective data, the subjective data are mainly from questionnaire designed based on the evaluation dimensions and user interview conducted before and after the experiment. While the objective data are consisted of Electrocardiogram (ECG), reaction time, numbers of reaction error and the video data recorded during the experiment. For the analysis of data, we calculate the integrated score of each evaluation dimension by using factor analysis. In order to improve the credibility of the assessment, we use the ECG signal and reaction test data before and after experiment to validate the changes of fatigue during the experiment, and the typical behavioral features extracted from the experiment video to explain the result of subjective questionnaire. Experimental results show that the System has a better user experience and learning performance, but slight visual fatigue exists after experiment.