Zanthoxylum bungeanum is an economically important crop worldwide due to its high content of aroma-producing monoterpenoids, and development of varieties with enhanced flavor and overall quality is a crucial research area. However, the transcriptional regulatory mechanisms underlying monoterpenoid synthesis in Z. bungeanum remain unclear, hindering these breeding efforts. In this study, RNA sequencing, gas chromatography–mass spectrometry, and other molecular biology techniques were used to identify the underlying transcriptional regulation mechanisms. Two transcription factors, ZbbHLH2 and ZbERF6, were identified as key regulators of monoterpenoid synthesis in Z. bungeanum that upregulate various monoterpenoid synthesis-associated genes and are novel transcriptional activators of ZbIDI, which encodes the rate-limiting enzyme in plant monoterpenoid synthesis. Functional analysis revealed that the expression of three genes [1] modulates monoterpenoid accumulation in Z. bungeanum peel. These findings provide novel insights into the metabolic regulatory network of monoterpenoid synthesis in Z. bungeanum peel, offer potential strategies for the biofortification of specific monoterpenoids, and will promote the development of Z. bungeanum germplasm for targeted breeding and quality improvement.