Tall clonal grasses commonly display competitive advantages with nitrogen (N) enrichment. However, it is currently unknown whether their height is derived from the vegetative or reproductive module. Moreover, it is unclear whether the height of the vegetative or reproductive system regulates the probability of extinction and colonization, and determines species richness (frequency). In this study, the impacts on clonal grasses were studied in a field experiment employing two frequencies (twice a year or monthly) crossed with nine N addition rates in a temperate grassland. We found that the N addition decreased species frequency and increased extinction probability, but did not change the species colonization probability. A low frequency of N addition decreased species frequency and colonization probability, but increased extinction probability. Species reproductive height is the best index to predict the extinction probability of clonal grasses in N-enriched conditions relative to the vegetative height, average height, and species biomass. No significant relationships were detected between plant height and species colonization probability. The low frequency of N addition may overestimate the negative effect from N deposition on clonal grass diversity, suggesting that a higher frequency of N addition is more suitable in assessing the ecological effects of N deposition. Moreover, this study illustrates that reproductive height, not the vegetative height, was associated with the clonal species extinction probability under N-enriched environment.