Ginkgo biloba (ginkgo) is a well-known ornamental tree. The yellow-leaf ginkgo mutant is an ideal material for studying leaf pigment synthesis and mutation. In this study, we used the Illumina sequencing of ginkgo small RNAs to gain insight into the function of microRNAs (miRNAs) in leaf color mutation. We constructed six small RNA libraries, and identified a total of 426 known and 265 novel miRNAs. Nineteen differentially expressed miRNAs (DEMs) were detected between the yellow-leaf and the green-leaf groups, including 8 upregulated miRNAs. The target genes of DEMs were predicted, resulting in the identification of 205 target mRNAs and 230 target gene binding sites. We found that the novel 158_mature and gma-miR2118a-3p target genes were involved in pigment biosynthesis. Three miRNAs, the novel 151_mature, ptc-miR396e-3p and aly-miR156a-5p appeared to be the potential key regulators of leaf color mutation. These DEMs and their corresponding target genes likely play key roles in the regulation of the yellow-leaf mutant. This study constructed miRNA profiles and provides new insight and a reference for related studies on miRNA regulation of leaf color pigment synthesis.