As the status indicator of system programs, loading icons have a significant role in human–computer interaction. This study explored the effect of the visual presentation of mobile application loading icons on users' time perception and emotion. The two variables adopted in this experiment were the type of loading icons and the animation frequencies. Three types of loading icons were used: circle type, aligned dots type, and logo type. Four frequencies were chosen: 3 Hz, 2 Hz, 1.5 Hz, and 1 Hz (changing every 333 ms, 500 ms, 666 ms, and 1000 ms). Theories related to subjective temporal experience and the three-dimensional emotion model of pleasure-arousal-dominance were utilized in this experiment to measure the user's time perception and emotion comprehensively. The experiment in this study was a 3x4 within-subject design. A total of 67 university students aged 18–26 participated in this experiment. The results showed that users' time perception and emotions were influenced by icon types and animation frequencies. Users who experience logo type icons were more inclined to generate positive evaluations. Loading icons with higher animation frequency had more positive user perception evaluation, but for more complex icons, excessively high animation frequency probably led to a negative visual experience. These findings might help improve the waiting experience of users when using the applications.