Habitat heterogeneity is a basic characteristic of natural ecosystem. The essential resources and environmental factors for plant growth are highly spatiotemporal heterogeneity. Clonal plants are plants with the clonal characteristics under natural condition, which can produce asexual reproduction through buds, rhizomes, tillers or branches connected with the mother plant. Once these propagules settle down, they can become potential independent individuals. They can adapt to the heterogeneous habitats through their unique habitat adaptation strategies (including morphological plasticity, clonal integration, clonal division of labor, foraging behavior, etc.) to obtain resources from heterogeneous habitats or avoid stress to the greatest extent. Based on analysis of the different characteristics of habitat heterogeneity in different classification criteria, this paper holds that habitat heterogeneity can be divided into temporal heterogeneity and spatial heterogeneity, or resource heterogeneity and environmental heterogeneity in terms of habitat function. Meanwhile, the adaptive strategies of the clonal plants in different resource heterogeneous habitats (light, nutrient, and water) or heterogeneous stress conditions (saline alkali stress, sand burial and heavy metal stress) were reviewed. Finally, the adaptation strategies of clonal plants to heterogeneous habitats were summarized. The suggestions for future research directions were put forward. (1) In the future research, we should consider combining the variation characteristics of habitat factors with spatial heterogeneity to explore the response characteristics of clonal plants more comprehensively. It is necessary to analyze the characteristics of clonal plants to habitat heterogeneity in different growth stages from the perspective of field in-situ control and long-term monitoring. (2) The previous studies have focused on the responses of clonal plants to abiotic heterogeneity (such as nutrients). However, soil biological factors (soil animals and soil microorganisms) also play an important role in regulation, and may even reshape the response of clonal plants in nature. (3) The invasion mechanism of clonal plants should also be deeply researched. (4) The application potential of clonal plants in ecosystem restoration should be widely concerned in future research.