The nine-axis inertial and measurement unit (IMU)-based three-dimensional (3D) orientation estimation is a fundamental part of inertial motion capture. Recently, owing to the successful utilization of deep learning in various applications, orientation estimation neural networks (NNs) trained on large datasets, including nine-axis IMU signals and reference orientation data, have been developed. During the training process, the limited amount of training data is a critical issue in the development of powerful networks. Data augmentation, which increases the amount of training data, is a key approach for addressing the data shortage problem and thus for improving the estimation performance. However, to the best of our knowledge, no studies have been conducted to analyze the effects of data augmentation techniques on estimation performance in orientation estimation networks using IMU sensors. This paper selects three data augmentation techniques for IMU-based orientation estimation NNs, i.e., augmentation by virtual rotation, bias addition, and noise addition (which are hereafter referred to as rotation, bias, and noise, respectively). Then, this paper analyzes the effects of these augmentation techniques on estimation accuracy in recurrent neural networks, for a total of seven combinations (i.e., rotation only, bias only, noise only, rotation and bias, rotation and noise, and rotation and bias and noise). The evaluation results show that, among a total of seven augmentation cases, four cases including ‘rotation’ (i.e., rotation only, rotation and bias, rotation and noise, and rotation and bias and noise) occupy the top four. Therefore, it may be concluded that the augmentation effect of rotation is overwhelming compared to those of bias and noise. By applying rotation augmentation, the performance of the NN can be significantly improved. The analysis of the effect of the data augmentation techniques presented in this paper may provide insights for developing robust IMU-based orientation estimation networks.