Low temperature is a major factor affecting rice geographical distribution growth, development, and productivity. Cold stress mediates a series of physiological and metabolite changes, such as alterations in chlorophyll fluorescence, electrolyte leakage, reactive oxygen species (ROS), malondialdehyde (MAD), sucrose, lipid peroxides, proline, and other metabolites, plant endogenous hormones abscisic acid (ABA) and gibberellin (GA) also changes. In this review, we summarize the recent research progress on physiological and metabolic changes under low temperature, cold stress related loci and QTL reported by map-based cloning and genome-wide association analysis (GWAS), and some molecular mechanisms in response to low temperature in rice. We also discuss the future prospects on breeding cold tolerance varieties of rice.