Abstract: Rhizosphere microorganisms endow plants with stress resistance, and variations in their community structure and ecological functions reflect the adaptability of crops to environmental changes. Domestication affects the genetic diversity, physiological traits, and crop metabolites, affecting the composition and function of rhizosphere microbial communities. To date, studies on crop domestication have mainly focused on the correlation and influencing mechanisms between plant genetic diversity and plant phenotypic and physiological characteristics. However, the role of microorganisms in crop domestication and exploration of interactive mechanisms with plants are still in their infancy. In this review, we systematically summarize the current progress regarding the effects of domestication on the community construction of gramineous crop rhizosphere microorganisms. Therefore, we focused on foxtail millet, an important C4 model plant originating in China, to discuss the effects of domestication on foxtail millet growth and physiological traits and how these changes may further affect the structural and functional properties of rhizosphere microbial communities. This review provides theoretical guidance for the restoration of beneficial crop-microbe relationships in agricultural ecosystems.