Cotton (Gossypium spp.) has become an important economic crop for human cultivation because of its ultra-long fiber cells produced specifically from seed epidermis. To date, multi-omics approaches, such as multi-strategic transciptome analysis, cDNA microarray, RNA-seq, small RNA-seq, and single-cell transcriptome sequencing, have been applied to dig into the mechanisms of fiber development, regulations of metabolite biosynthesis, and different ways to improve cotton breeding processes. Transcriptome studies using early cotton fiber initiation found more than 5000 differentially expressed genes (DEGs) in wild type and fl mutants, of which about 1800 genes were upregulated and nearly 3600 genes were downregulated. Further gene co-expression network analysis integrated five important regulatory modules that may be involved in fiber development. Various genome editing techniques, including CRISPR/Cas9, Cas12, and cytidine base editing, have been applied to study the potential biological functions of a given candidate gene suspected to play a role during fiber formation. On this basis, the regulatory network of cotton fiber cell development was preliminarily mapped. The MYB-bHLH-WDR (MBW) transcription factor complex and auxin and brassinolide response genes play a role in regulating fiber initiation. A variety of signaling molecules, including ethylene and ultra-long-chain fatty acids, form a complex regulatory network that mediates fiber elongation. Multistage transcription factors regulating CesA4, 7, and 8 specifically directed the precipitation of secondary cell wall of cotton fibers. Furthermore, through continuous research on the synthesis of cotton secondary metabolites, gossypol, cotton pest and abiotic stress response, plant morphology regulation, seed oil separation and utilization, many high-quality genes related to breeding have been identified, which have important guiding significance for the future breeding and creation of cotton varieties. Here, we try to summarize the important research results of cotton molecular biology in recent decades, hoping that the chapter can provide some ideas and exploration directions for scholars in the future study of cotton plants.