Abstract: Cotton is one of the most widely cultivated cash crops in agriculture and textile industry worldwide. Innovative techniques have emerged to enhance the efficiency of cotton production in recent years. Among them, laser ablation can be expected to treat the cotton terminal buds in modern agriculture. The cotton terminal dominance can also be suppressed for the desired topping. Both the yield and quality of the cotton crop are improved to save the plant’s energy and resources towards the development of cotton bolls. Compared with traditional mechanical pruning, laser ablation can minimize the mechanical damage to the plant, which can often occur during physical pruning sensitive to pests and diseases. Moreover, the extensive use of chemical growth regulators can be avoided from agricultural practices to control plant growth. The environmental impact can be reduced to support healthy crop production in sustainable agriculture. Laser ablation can enhance the production potential after the treatment of cotton terminal bud. This study aims to examine the impact of the temperature field on the cotton terminal buds during laser ablation. A series of experiments were conducted to determine the thermal properties of cotton. A time-varying temperature field model was developed for the laser ablation using COMSOL Multiphysics finite element software. The heat transfer was then used to simulate the temperature distribution in the cotton shoot terminal meristems during laser ablation. There were great variations in the temperature both along the diameter and depth directions of the cotton shoot terminal meristem. A systematic investigation was also made to explore the effect of laser ablation on the surface erosion of the shoot terminal meristems. Finally, the numerical model was verified to be highly effective in the simulation. The results revealed that the ablation time was reduced by 45.55% and 67.36%, respectively, at the laser powers of 40 and 50 W, compared with the standard laser power of 30 W. Furthermore, the maximum temperature of the cotton shoot terminal meristems decreased with an increase in the laser spot size. Specifically, the ablation temperature reached in just 0.50 s, with a time reduction of 76.85% at a 2.5 mm spot size, compared with a 3.5 mm spot size. The higher water content further increased the ablation time. For instance, the reach time of the ablation temperature was 0.52 s at a water content of 75%, 17.31% faster than that at 95% water content. The speed of heat diffusion along the diameter direction was significantly higher than that along the depth direction under constant laser power. There was also the directional heat transfer of the laser ablation. Experimental results showed that a 50 W laser power with a 1 second ablation time significantly facilitated the growth of the shoot terminal meristems. However, the growth was effectively suppressed at a 100 W laser power with 1 second of ablation. Moreover, the greater the degree of carbonization and ablation was, the more pronounced the inhibitory effect on the shoot growth was. This finding can also provide valuable insights into the practical applications of laser ablation in cotton cultivation.