Climate change (rainfall events and global warming) affects the survival of alfalfa (Medicago sativa L.) in winter. Appropriate water management can quickly reduce the mortality of alfalfa during winter. To determine how changes in water affect the cold resistance of alfalfa, we explored the root system traits under different rainfall events and the effects on cold resistance in three alfalfa cultivars. These were exposed to three simulated rainfall events (SRE) × two phases in a randomized complete block design with six replications. The three cultivars were WL168, WL353 and WL440, and the three SRE were irrigation once every second day (D2), every four days (D4) and every eight days (D8). There were two phases: before cold acclimation and after cold acclimation. Our results demonstrated that a period of exposure to low temperature was required for alfalfa to achieve maximum cold resistance. The root system tended toward herringbone branching under D8, compared with D2 and D4, and demonstrated greater root biomass, crown diameter, root volume, average link length and topological index. Nevertheless, D8 had less lateral root length, root surface area, specific root length, root forks and fractal dimensions. Greater root biomass and topological index were beneficial to cold resistance in alfalfa, while more lateral roots and root forks inhibited its ability to survive winter. Alfalfa roots had higher proline, soluble sugar and starch content in D8 than in D2 and D4. In contrast, there was lower malondialdehyde in D8, indicating that alfalfa had better cold resistance following a longer irrigation interval before winter. After examining root biomass, root system traits and physiological indexes we concluded that WL168 exhibited stronger cold resistance. Our results contribute to greater understanding of root and cold stress, consequently providing references for selection of cultivars and field water management to improve cold resistance of alfalfa in the context of changes in rainfall patterns.