Understanding the impact of the warming trend on phenological stages and phases of cotton (Gossypium hirsutum L.) in central and lower Punjab, Pakistan, may assist in optimizing crop management practices to enhance production. This study determined the influence of the thermal trend on cotton phenology from 1980–2015 in 15 selected locations. The results demonstrated that observed phenological stages including sowing (S), emergence (E), anthesis (A) and physiological maturity (M) occurred earlier by, on average, 5.35, 5.08, 2.87 and 1.12 days decade−1, respectively. Phenological phases, sowing anthesis (S-A), anthesis to maturity (A-M) and sowing to maturity (S-M) were reduced by, on average, 2.45, 1.76 and 4.23 days decade−1, respectively. Observed sowing, emergence, anthesis and maturity were negatively correlated with air temperature by, on average, −2.03, −1.93, −1.09 and −0.42 days °C−1, respectively. Observed sowing-anthesis, anthesis to maturity and sowing-maturity were also negatively correlated with temperature by, on average, −0.94, −0.67 and −1.61 days °C−1, respectively. Applying the cropping system model CSM-CROPGRO-Cotton model using a standard variety in all locations indicated that the model-predicted phenology accelerated more due to warming trends than field-observed phenology. However, 30.21% of the harmful influence of the thermal trend was compensated as a result of introducing new cotton cultivars with higher growing degree day (thermal time) requirements. Therefore, new cotton cultivars which have higher thermal times and are high temperature tolerant should be evolved.