Abstract Small Auxin Upregulated RNA (SAUR) genes constitute the largest family of early auxin-responsive genes and are critically involved in plant growth and development. However, their functional roles in root morphogenesis and terpenoid metabolism, particularly in gymnosperms, remain largely unexplored. In this study, we identified 58 SAUR genes in the Ginkgo biloba genome and performed comprehensive analyses of their phylogenetic relationships, gene structures, conserved motifs, and chromosomal distributions. Most GbSAUR genes lack introns and contain conserved auxin-responsive elements, suggesting a potential for rapid transcriptional activation in response to auxin signaling. Notably, GbSAUR48 exhibited high and specific expression in root tissues. Functional characterization revealed that overexpression of GbSAUR48 in G. biloba significantly enhanced lateral root formation and increased the accumulation of ginkgolides A (GA) and B (GB). Conversely, virus-induced gene silencing (VIGS) of GbSAUR48 suppressed lateral root development and reduced terpenoid lactone content. Further quantitative real-time PCR (qRT-PCR) analysis showed that key genes involved in ginkgolide biosynthesis, GbCYP7005C1, GbCYP7005C3, and GbCYP867E38, were upregulated in overexpression lines and downregulated in silenced plants. These findings indicate that GbSAUR48 plays a dual regulatory role in promoting both lateral root development and terpenoid lactone biosynthesis. This study provides novel insights into the multifunctionality of SAUR genes in gymnosperms and highlights their importance in regulating secondary metabolism in G. biloba.