Study on modules of clonal populations has important theoretical and practical significance to understand the survival regularity and environmental adaptation mechanisms. The grey system theory was used to analyze correlations between environmental factors and the modular structure of clonal populations of Calligonum mongolicum in the Minqin desert at genet, ramet and branch system levels. The results showed that: 1) Heights of genet and ramet could reflect the development status and environment adaptability and indicate the growth state of the modules of the clonal population. 2) The ramet had more significant effects on the whole modular structure than the genet. 3) The first grade branch system was the foundation for the whole clonal plant. The internal correlation analysis showed that diameter growth and length growth coordinated with each other. The second grade branch system had limited impact and could be taken as a transition system. The third grade branch system significantly influenced the present year branch system whose growth was dependent on both the first grade and third grade branches. 4) The correlation among the modules showed a strong hierarchy, indicating that the whole pattern of the modular structure was relatively reasonable, and the population had strong adaptability to environment. 5) There were close correlations between the 16 environmental factors in study and the modules. Climate factors played a crucial role, soil bulk density and the content of soil organic matter also strongly affected the growth and development of C. mongolicum, and the soil moisture content was also a relatively sensitive factor.