Medicago sativa is a high-quality legume forage that is widely cultivated around the world. However, low phosphorus (LP) stress is one of the main limiting factors for its yield and quality. Currently, it is unclear how various alfalfa root types respond to LP stress. Thus, the creeping-rooted M. varia 'Gannong No. 4' (or GN), tap-rooted M. sativa 'Longdong' (or LD), and rhizomatous-rooted M. sativa 'Qingshui' (or QS) were selected to detect changes in growth, metabolites, phytohormones, and organic acids after 34 days of LP stress treatment (0.01 mmol·L−1 KH2PO4). We observed LP stress significantly inhibited plant growth, and 123, 73, and 42 considerably upregulated differential metabolites were categorized into 33, 26, and 20 metabolic pathways in GN, LD, and QS under LP stress, respectively. Amino acids, plant growth regulators, and organic acids are the main metabolites. After 34 d of LP treatment, the plant height, total surface area, leaf length, ground biomass, leaf width, total volume, leaf area, and ZT content of different root types of alfalfa significantly decreased, while the contents of malic acid, citric acid, oxalic acid, IAA, ABA, and GA3 significantly increased. The plant height, leaf length, leaf width, leaf area, total surface area, total volume, ground biomass, root biomass, the number of different metabolites, and the contents of malic, citric, and oxalic acid, and IAA of GN were significantly higher than those of QS and LD under LP stress. From this point of view, GN was more tolerant than LD and QS under the LP condition. [ABSTRACT FROM AUTHOR]