Pepper is a major horticultural crop cultivated extensively worldwide. Among its various agronomic characteristics, fruit length is a key trait influencing both yield and visual quality. Despite its importance, the genetic mechanisms regulating fruit length in Capsicum remain insufficiently characterized, hindering the development of high-yielding and aesthetically desirable cultivars. In this study, fruits at three developmental stages (0, 15, and 30 days after flowering) were sampled from the long-fruit mutant fe1 and its wild-type progenitor LY0. Phenotypic characterization and transcriptomic sequencing were conducted to identify candidate genes associated with fruit length regulation. Morphological analysis revealed that the most pronounced difference in fruit length occurred at 30 days after flowering. RNA-seq analysis identified 41,194 genes, including 13,512 differentially expressed genes (DEGs). Enrichment analysis highlighted key pathways, such as plant–pathogen interaction, plant hormone signal transduction, and the MAPK signaling pathway. DEG classification suggested that several downregulated genes related to early auxin responses may contribute to the regulation of fruit elongation. Notably, the gibberellin signaling gene SCL13 (Caz12g26660), transcription factors MYB48 (Caz11g07190) and ERF3-like (Caz10g00810), and the cell-wall-modifying gene XTH15-like (Caz07g19100) showed significantly elevated expression in 30-day-old fruits of fe1. Weighted gene co-expression network analysis (WGCNA) further revealed a strong positive correlation among these genes. Quantitative RT-PCR analysis of eight selected DEGs confirmed the RNA-seq results. This study provides a foundational framework for dissecting the molecular regulatory network of fruit length in Capsicum, offering valuable insights for breeding programs.