Winter dormancy (WD) is the most crucial strategy for plants as they must cope with potentially deadly environments. In recent decades, this process in economically important perennial eudicots has been extensively studied due to changing climates. However, in evergreen monocots without chilling requirements, dormancy processes are so far a mystery. We compared the WD process in closely related evergreen and deciduous iris species across critical developmental stages. Both species exhibit a peculiar “shallow WD” with distinct durations, and could easily resume growth under warm conditions. Combining results from the multipronged approach, SVP/DAM or FUL/AP1 from MADS-box was associated with dormancy- or growth-related module, respectively, and coexpressed with important pathways. Also, gene expression patterns and physiological changes highlighted potential ABA and JA antagonism in coordinating growth and stress responses, while differences in carbohydrate metabolism and reactive oxygen species scavenging contributed to species-specific “shallow WD” durations. Moreover, a detailed analysis of MIKCC MADS-box in irises revealed common features in eudicots and possible new roles for members in perennial monocots during “shallow WD.” In essence, our results not only provide a portrait of a peculiar WD process in perennial monocots but also offer new insights into the regulatory mechanism underlying WD in plants.