Cotton, one of the most important and widely grown crops in the world, is a well-traded agricultural commodity primarily for textile fiber purposes. In addition, cottonseed (a byproduct of fiber production) has been used as an agro-based raw material for manufacturing bio-friendly and sustainable products. Qualitative and quantitative characterization of cotton biomass products/byproducts is an important research area for quality monitoring, improvement, and enhanced use. Fourier transform infrared (FT-IR) spectroscopy is a nondestructive instrumental technique widely used in applied cotton fiber and cottonseed research. This review synthesizes and analyzes the latest developments using FT-IR spectroscopy in investigation of cotton fiber and three cottonseed components (oil, meal/protein, hull) that are impacted by various genetic, cropping, post-harvest processing, and end-use parameters and conditions. Increased knowledge from this review could provide insight and vision in future FT-IR research for the chemistry and quality-evolving mechanisms of these cotton biomass products and their end-uses.