Dioecious plants have different needs for natural resources due to sex differences, which can lead to skewed sex ratios. Clonal growth facilitates and optimizes resources of clonal plants. So, dioecious plants show inter-sex differences in clonality. However, it is unclear how the clonality varies between female and male plants when they exhibit skewed sex ratios along an altitudinal gradient. Here, we investigated the sex ratio and clonality of Hippophae tibetana populations growing at three altitudes in the alpine meadow. We founded that (i) H. tibetana growing at different altitudes mainly consisted of II and III age classes, with a significantly male-biased sex ratio observed at a low altitude, a female-biased ratio at a middle altitude, and no significant sex-bias in the population at a high altitude. (ii) The population distribution was generally random at both low and high altitudes, while clustered at middle altitudes with an increasing scale. Meanwhile, the male and female populations at a low altitude showed a negative correlation, while the male and female at a middle altitude only showed a negative correlation at a 0–0.5 m scale, and spatial independence with increasing scales. (iii) Females of H. tibetana had a strong clonal capacity than male plants at a middle altitude, while the opposite was observed at a low altitude. The number of males of H. tibetana growing at a low altitude and with higher clonal diversity were higher than females at mid altitude. Our findings will contribute to the understanding of the sexual dimorphism exhibited by dioecious plants as well as the importance of a clonal adaptation in response to environmental change.