AbstractCotton fibers, derived from the epidermis of the ovule, provide a sustainable natural fiber source for the textile industry. Traits related to fiber yield are predominantly determined by molecular regulations in the epidermis of the outer integument (OI) region of the cotton ovule. Here, we identify an R2R3 MYB transcription factor coding gene GhLPF1 within the QTL‐LP‐ChrA06 locus for lint percentage (LP, percentage of lint to seed cotton) through constructing the 1‐Day Post Anthesis Cotton Ovule Spatial Transcriptome Atlas. GhLPF1 is subjected as a downstream target of miR828 during fiber development. The direct downstream genes (DDGs) of GhLPF1 are biased to increased expression in GhLPF1‐CR, and are preferentially expressed in OI, so that GhLPF1 is primarily a transcriptional repressor to its DDGs. Population‐wide transcriptome analysis confirms that expression variation of GhLPF1‐DDGs is significantly biased to negative correlation with LP, among which a type I homeobox protein‐coding gene GhHB6 is further validated to be the directly downstream gene of GhLPF1. Given these data, it is demonstrated that GhLPF1 mediates a regulation network in LP as a transcriptional repressor, which makes it a valuable functional marker for fiber‐trait improvement application from QTL‐LP‐ChrA06.