As low temperature is a crucial contributing factor to the albino peculiarity of young leaves of White Leaf No.1 (WL-1), the chilling tolerance of its functional leaves should be considered simultaneously. Alteration of DNA methylation (an epigenetic regulator) due to chilling has been often observed in plants, but little is known about whether glycinebetaine (GB, a potential methyl donor) is linked to gene methylation priming responses of plants to low temperature. Herein, we provided evidence for the regulation of gene methylation by GB, which in turn affects the apparent characteristics of WL-1 functional leaves under low temperature condition. Results showed that the transpiration efficiency and chlorophyll levels of WL-1 functional leaves were significantly increased by GB application under low temperature condition. GB affected WL-1 response to low temperature by increasing the methylation level of most of the methytransferase and demethylase genes, PSⅡ structure genes, and some of the chlorophyll synthesis genes, which were further proved by multivariate analyses. Additionally, the number of methylated gene sites was increased by GB under low temperature. Present study suggests important roles of GB in enhancing photosynthesis of albino tea functional leaves under low temperature condition by regulating related gene methylation.