The CROPGRO-Cotton model was first calibrated and validated with the six years (2011-12 to 2016-17) of experimental data collected at Regional Research Station, A.A.U., Anand for two cultivars of cotton (DCH 32 and G. Cot. Hy. 102) to study the effect of intra-seasonal climatic variability on seed cotton yield. The model sensitivity analysis was carried out by incremental change in climatic parameters (maximum and minimum temperature from -30 to +30C) and rainfall (-25% to +25%). Results revealed that elevated temperature had negative effect on seed cotton yield and reduced temperature had positive effect on seed cotton yield. The varieties DCH 32 was slightly less affected by the temperature variation than G. Cot. Hy. 102. Temperature variation during October to December was found to have maximum effect on cotton crop. The effect of minimum temperature on seed cotton yield was more than that observed with maximum temperature.Cotton crop was affected more by variation in rainfall during September in comparison to that of July and August.