During continuous use of displays, a short rest can relax users’ eyes and relieve visual fatigue. As one of the most important devices of virtual reality, head‐mounted displays (HMDs) can create an immersive 3D virtual world. When users have a short rest during the using of HMDs, they will experience a transition from virtual world to real world. In order to investigate how this change affects users’ eye condition, we designed a 2 × 2 experiment to explore the effects of short rest during continuous using of HMDs and compared the results with those of 2D displays. The Visual Fatigue Scale, critical flicker frequency, visual acuity, pupillary diameter, and accommodation response of 80 participants were measured to assess the subject’s performance. The experimental results indicated that a short rest during the using of 2D displays could significantly reduce users’ visual fatigue. However, the experimental results of using HMDs showed that short rest during continuous using of HMD induced more severe symptoms of subjectively visual discomfort, but reduced the objectively visual fatigue.