The aim of this study was to investigate the effect of guanidinium nonaborate (GB) and imidazolium borate (IB) on thermal stability and flammability properties of cotton fabrics. The flame retardant and thermal stability properties of treated cotton fabrics were investigated using limiting oxygen index (LOI) and thermogravimetric analysis. The residues remained after LOI test were characterized by conducting attenuated total reflectance-Fourier-transform infrared spectroscopy and scanning electron microscopy with a wavelength-dispersive X-ray spectrometer. The results showed that both boron compounds increased the LOI value of cotton fabric as the amount increased by several combined flame retardant effects. IB-treated cotton fabrics had higher LOI value than GB-treated ones due to the higher increment in char yield which was the predominant flame retardant action of both boron compounds.