The major cultivated varieties of adlay generally exhibit late flowering and excessive plant height, which are important factors restricting their yield stability and adaptability. Previous studies have identified that a 38-bp insertion variation in the promoter region of ClCCT is a key genetic locus regulating flowering time and plant height. To clarify the application potential of this variation in breeding, this study analyzed its pleiotropic effects on flowering time, plant height, stem-leaf traits, and grain traits using near-isogenic lines (NILs), and conducted phenotypic verification and evaluation in a pyramiding breeding population. The results showed that in the NILs, the 38-bp insertion variation significantly promoted earlier flowering and reduced plant height, while also exerting regulatory effects on stem-leaf and grain traits. Among the 65 early-flowering and dwarf lines obtained from the pyramiding breeding population, the frequency of the insertion-type allele reached as high as 72.3%. Compared with the heterozygous/deletion lines, the insertion-type lines showed significantly advanced flowering time, while no significant differences were observed in plant height, stem-leaf traits, and grain traits, indicating that under complex genetic backgrounds, this variation primarily regulates flowering time with limited effects on other agronomic traits. Integrating data from both populations indicates that the regulatory effect of the 38-bp insertion variation on flowering time is stable across different genetic backgrounds. Moreover, owing to the ease of detection, this marker can serve as an efficient tool for marker-assisted selection (MAS) of flowering time in adlay.