Abstract: Cotton plays a critical role in both the global and Chinese agricultural sectors. As one of the most widely cultivated cash crops, cotton is a major source of livelihood for millions of farmers worldwide. It is an essential crop in agricultural practices, fulfilling domestic textile needs while also contributing significantly to the export economy. In China, cotton is not only a key agricultural product but also a crucial component of the nation’s textile industry, making its cultivation and management a vital concern for farmers and policymakers alike. In recent years, innovative agricultural techniques have emerged to enhance cotton production efficiency. One such method is the use of laser ablation technology in treating cotton terminal buds, which represents a promising advancement in modern agricultural management. By applying laser ablation to cotton terminal buds, terminal dominance can be suppressed, leading to the desired topping effect. This process redirects the plant’s energy and resources towards the development of cotton bolls, which can improve both the yield and quality of the cotton crop. Laser ablation technology offers several distinct advantages over traditional mechanical pruning methods. For one, it minimizes the risk of mechanical damage to the plant, which often occurs during physical pruning and can open the plant to pests and diseases. Moreover, laser ablation eliminates the need for the extensive use of chemical growth regulators, which are commonly employed in traditional agricultural practices to control plant growth. This not only reduces the environmental impact but also supports the sustainable development of agriculture by promoting healthier crop production methods. The significance of laser ablation in cotton terminal bud treatment lies not only in its ability to enhance cotton production but also in its potential to revolutionize agricultural practices. This makes it an important step forward in the quest for modern, sustainable agricultural solutions. To examine the impact of temperature on cotton terminal buds during the laser ablation process, this study conducted a series of experiments to determine the thermal properties of cotton. Building on heat transfer theory, the study used the COMSOL Multiphysics finite element analysis software to develop a time-varying temperature field model for the laser ablation process. The model was used to simulate the temperature distribution in cotton shoot terminal meristems during laser ablation, focusing on the variations in temperature both along the diameter and depth directions of the cotton shoot terminal meristem. Additionally, the study investigated how laser ablation affects the surface erosion of cotton shoot terminal meristems. The results from the model verification indicate that the numerical model is highly effective for simulating laser ablation of cotton shoot terminal meristems. At laser powers of 40W and 50W, the ablation time was reduced by 45.55% and 67.36%, respectively, compared to the standard 30W laser power. Furthermore, the maximum temperature of the cotton shoot terminal meristems decreased with an increase in the laser spot size. Specifically, at a 2.5mm spot size, the ablation temperature was reached in just 0.50 seconds, a time reduction of 76.85% compared to a 3.5mm spot size. The study also revealed that higher water content could further reduce the ablation time. For instance, at a water content of 95%, the time to reach the ablation temperature was 0.52 seconds, 17% faster than at 75% water content. In terms of heat diffusion, the model indicated that, under constant laser power, the heat diffusion speed along the diameter direction was significantly higher than that along the depth direction, highlighting the directional heat transfer characteristics of the laser ablation process. Experimental results showed that, for cotton shoot terminal meristems, a 50W laser power with a 1-second ablation time did not significantly inhibit the growth of the shoot terminal meristems. However, at a 100W laser power with 1 second of ablation, the growth of the cotton shoot terminal meristems was effectively suppressed. Moreover, the greater the degree of carbonization and ablation, the more pronounced the inhibitory effect on shoot growth. This study provides valuable insights into the theoretical and practical applications of laser ablation technology in cotton cultivation.