Dichondra (Dichondra repens) is an important ground cover plant for landscaping and establishment of green space, but adaptive mechanism of drought tolerance is not well understood in this species. This study was conducted to compare differential response to drought stress among three genotypes (Dr5, Duliujiang, and Dr29) based on integrated physiological, ultrastructural, and metabolic assays. Results showed that drought significantly inhibited photosynthesis, accelerated lipids peroxidation, and also disrupted water balance and cellular metabolism in dichondra plants. Dr5 showed better photochemical efficiency of photosystem II and water homeostasis, less oxidative damage, and more stable chlorophyll metabolism than Duliujinag or Dr29 in response to drought stress. In addition, Dr5 accumulated more amino acids, organic acids, and other metabolites, which was good for maintaining better antioxidant capacity, osmotic homeostasis, and energy metabolism under drought stress. Drought tolerance of Duliujiang was lower than Dr5, but better than Dr29, which could be positively correlated with accumulations of sucrose, maltitol, aconitic acid, isocitric acid, and shikimic acid due to critical roles of these metabolites in osmotic adjustment and metabolic homeostasis. Current findings provide insights into understanding of underlying mechanism of metabolic regulation in dichondra species. Dr5 could be used as an important drought-tolerant resource for cultivation and water-saving breeding.