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<i>Quercus aliena</i> is an economically important tree species and one of the dominant native oak species in China. Although its leaves typically turn yellow in autumn, we observed natural variants with red leaves. It is important to understand the mechanisms involved in leaf color variation in this species. Therefore, we compared a <i>Q. aliena</i> tree with yellow leaves and three variants with red leaves at different stages of senescence in order to determine the causes of natural variation. We found that the accumulation of anthocyanins such as cyanidin 3-<i>O</i>-glucoside and cyanidin 3-<i>O</i>-sambubiglycoside had a significant effect on leaf coloration. Gene expression analysis showed upregulation of almost all genes encoding enzymes involved in anthocyanin synthesis in the red-leaved variants during the early and main discoloration stages of senescence. These findings are consistent with the accumulation of anthocyanin in red variants. Furthermore, the variants showed significantly higher expression of transcription factors associated with anthocyanin synthesis, such as those encoded by genes <i>QaMYB1</i> and <i>QaMYB3</i>. Our findings provide new insights into the physiological and molecular mechanisms involved in autumn leaf coloration in <i>Q. aliena</i>, as well as provide genetic resources for further development and cultivation of valuable ornamental variants of this species.