Time perception is the basis of cognitive processing, and it may be affected by depression levels. People with depression often report slower subjective time experience; however, whether depression levels affect time perception has not been determined. More than 300 million people of all ages suffer from depression globally, and this number might be much larger if people with subthreshold depression, which indicates that an individual has clinically relevant depressive symptoms without meeting the criteria for full-blown major depressive disorder, are included. In this study, we examined the behavioral characteristics of time perception in patients with clinical depression and individuals with subthreshold depression based on a temporal bisection within the range of 400–1600 ms. The data were then fitted to a sigmoidal curve in order to calculate the subjective bisection point and Weber ratios. In addition, the event-related potential (ERP) responses of time perception in individuals with subthreshold depression were recorded to explore the possible mechanisms. The results were as follows: (1) The Weber ratios of individuals in the clinical and subthreshold depression groups were higher than those in the control group. There was no significant difference in the subjective bisection point between either the subthreshold depression group or the clinical depression group and the control group. Both the clinical and subthreshold depression groups had longer reaction times in each duration, and they tended to overestimate short durations and underestimate long durations. (2) The levels of depression (both trait depression and state depression) were positively related to the Weber ratio, and there was no correlation between the bisection point and either trait depression or state depression. (3) The P2 amplitude of the subthreshold depression group showed a decreasing trend, and the latency of the contingent negative variation (CNV) was delayed. The amplitude of the late positive component of timing (LPCt) decreased at the duration of 400 ms, but there was no difference in N1 between the subthreshold depression group and the control group. The above results suggest that there were similar changes in time perception between the subthreshold depression group and the clinical depression group; moreover, as the degree of depression increased, subjects showed greater variation in time perception. The higher Weber ratios of the clinical and subthreshold depression groups imply changes in the subjects’ internal clock, and such changes might be caused by the lack of sufficient cognitive resources for participating in time processing, which is revealed by the lower P2 amplitude. In the subthreshold depression group, the longer reaction time, longer CNV peak latency, and smaller LPCt amplitude, which is the positive deflection followed by CNV, suggest that the subthreshold depression group also exhibited some changes in temporal decision processes. In addition, there was no evidence of changes in working memory for the subthreshold depression group in time perception, as there was no difference in the bisection point. The current study did not record ERP signals of individuals with clinical depression; thus, it is necessary to explore the neural mechanism of time perception in individuals with clinical depression in the future.