Background: Cotton gin trash (CGT) is a lignocellulosic residue that can be used in the production of cellulosic ethanol. In a previous research, the sequential use of ultrasonication, liquid hot water, and ligninolytic enzymes was selected as pretreatment for the production of ethanol from CGT. However, an increment in the ethanol production is necessary. To accomplish that, this research evaluated the effect of pretreating CGT using alkaline ultrasonication before a liquid hot water and ligninolytic enzymes pretreatments for ethanol production. Three NaOH concentrations (5%, 10%, and 15%) were employed for the alkaline ultrasonication. Additionally, this work is one of the first applications of Fourier transform infrared (FT-IR) spectrum and principal component analysis (PCA) as fast methodology to identify the differences in the biomass after different types of pretreatments. Results: The three concentrations employed for the alkaline ultrasonication pretreatment produced ethanol yields and cellulose conversions higher than the experiment without NaOH. Furthermore, 15% NaOH concentration achieved twofold increment yield versus the treatment without NaOH. The FT-IR spectrum confirmed modifications in the CGT structure in the different pretreatments. PCA was helpful to determine differences between the pretreated and un-pretreated biomass and to evaluate how the CGT structure changed after each treatment. Conclusions: The combination of alkali ultrasonication hydrolysis, liquid hot water, and ligninolytic enzymes using 15% of NaOH improved 35% the ethanol yield compared with the original treatment. Additionally, we demonstrated the use of PCA to identify the modifications in the biomass structure after different types of pretreatments and conditions.