Previous studies have revealed that the visual system is highly sensitive to topological differences. Topological properties, which are first represented and processed, influence ongoing visual information processing. In addition, as a fundamental human ability, perception of duration can be affected by non-temporal information, including the magnitude, motion, and spatial frequency. Topological properties are another type of important non-temporal information, but little is known whether these can also affect duration perception. Recently, researchers have found that when an unexpected “oddball” stimulus is embedded in a train of repeated standard stimuli, its duration typically seems to be longer. This phenomenon is termed the oddball effect, and illustrates how duration perception can be affected by stimulus novelty. According to the topological approach to perceptual organization, the core intuitive notion of an object may be characterized precisely as topological invariance, and changes in topological properties will be regarded as the emergence of new objects by the vision system. Therefore, the impact of topological properties on duration perception of oddball stimuli was investigated in this research. In Experiment 1a 18 participants (7 men, 11 women) were asked to judge whether oddball stimuli (i.e., disks with one or two holes) were longer or shorter in duration than the standard stimuli (i.e., squares with one or two holes). In Experiment 1b, 14 participants (7 men, 7women) rated whether oddballs (i.e., disks with two holes, squares with one hole or squares with three holes)were longer or shorter in duration than standard stimuli (i.e., squares with two holes). Experiment 2 included 40 participants (15men, 25 women) and was designed to compare effects on duration perception of oddball stimuli between topological properties and other geometric properties. Participants were required to judge whether the oddballs (i.e., parallelograms, trapezoids, circles or rings) were longer or shorter in duration than standard stimuli (i.e., either squares or beeps of 1000 Hz). Results of Experiment 1 indicated that when there were topological differences between standard stimuli and the oddballs, the magnitude of the oddball effect was significantly larger than that of non-topological differences. Findings from Experiment 2 showed the magnitude of the oddball effect increased monotonically with increasing levels of stability of structural differences between standard stimuli and the oddballs. Compared with other geometrical properties, changes of topological properties induced the largest magnitude of oddball effect. These results suggest that topological properties are one type of important non-temporal information that affect duration perception of oddball stimuli. Furthermore, the current study supports the topological definition of perceptual objects.