Cotton textile dyeing consumes large amounts of energy and water and discharges large amount of wastewater and pollutants. Zero or less discharge of the wastewater and contaminants from the cotton textile dyeing has been under high demands from textile industry. Recently, a novel reactive dyeing technology of using a non-aqueous medium with little water (NMLW) was developed for cotton fabrics. However, the use of high concentration of reactive dyes in the system triggers aggregation of the dyes in cotton fibers, influencing the quality of dyed cotton textiles. In this investigation, adsorption, diffusion, and aggregation behavior of reactive dyes in cotton fibers were studied. Compared to traditional water-based dyeing system, cotton fabrics demonstrated superior color depth, as long with higher rates of dye uptake and fixation for reactive dyes. At low dye concentrations, the maximum absorption wavelengths of reactive dyes were unchanged, and complied with the Lambot-Beer law. However, when the dye concentration was excessively high, reactive dyes with different molecular structures, as well as multi-layer dye aggregates with π-π stacking and hydrogen bonding interactions, showed different light absorption spectral characteristics and photophysical properties. Moreover, the dye particle size and dye ionization were influenced by the dye concentration, molecular weight, molecular configuration, etc. Analysis of the molecular dynamics of reactive dyes revealed that the maximum dye aggregation size was predominantly dimer at low dye concentration. However, the dimer ratio significantly decreased, while the trimer ratio increased, and higher-order aggregates were observed at a higher dye concentration. The strength of hydrogen bonds between dye molecules and water molecules, as well as the number of water molecules surrounding dye molecules, was influenced by dye concentration and alkali. This study provides a foundation for understanding the micro-aggregation behavior of reactive dyes and offer guidance for optimizing the dyeing process in practical production settings.