Alfalfa (Medicago sativa L.) is a globally cultivated perennial forage legume. Flowering time, an important agronomic trait of alfalfa, is pivotal for farmers to determine the optimal harvest stage, thereby maximizing economic benefits. However, the underlying molecular basis of flowering time regulation in alfalfa remains unclear. Here we generated a comprehensive full-length, seasonal and diurnal transcriptome atlas comprising 108 samples, including two sets of late- and early-flowering alfalfa across spring, summer and autumn in the natural environment. A total of 389 candidate flowering time-related genes were identified in alfalfa, of which 92 were differentially expressed between early and late flowering plants. Further, we revealed that flowering time regulation genes predominantly identified in spring were mainly involved in vernalization, while genes exclusively identified in summer and autumn were primarily involved in circadian and photoperiodic pathways. Moreover, diurnal dynamics of transcriptomes demonstrate the precise orchestration of various biological processes, including chloroplast development, redox processes, biotic stress responses, growth and development, occurs at designated times throughout the day in accordance with external environmental cues. Together, our results provide a valuable resource for future manipulation of genetic control of flowering time in alfalfa, and demonstrate how plants adapt to diurnal and seasonal environments.