This paper presents a novel solution for estimating simulator sickness in HMDs using machine learning and 3D motion data, informed by user-labeled simulator sickness data and user analysis. We conducted a novel VR user study, which decomposed motion data and used an instant dial-based sickness scoring mechanism. We were able to emulate typical VR usage and collect user simulator sickness scores. Our user analysis shows that translation and rotation differently impact user simulator sickness in HMDs. In addition, users’ demographic information and self-assessed simulator sickness susceptibility data are collected and show some indication of potential simulator sickness. Guided by the findings from the user study, we developed a novel deep learning-based solution to better estimate simulator sickness with decomposed 3D motion features and user profile information. The model was trained and tested using the 3D motion dataset with user-labeled simulator sickness and profiles collected from the user study. The results show higher estimation accuracy when using the 3D motion data compared with methods based on optical flow extracted from the recorded video, as well as improved accuracy when decomposing the motion data and incorporating user profile information.