This study aimed to investigate the effects of pruning intensity on the growth and ecological functions of Eucalyptus 107 clone plantations, providing theoretical and practical guidance for scientific silvicultural management. A randomized block design was implemented at the Xiaoheijiang Base in Ning’er County, Pu’er City, Yunnan Province, with four pruning treatments: no pruning (control), pruning branches below 1/3 of the tree height, pruning branches below 1/2 of the tree height, and remove branches below 2/3 tree height. Growth parameters, including tree height, diameter at breast height (DBH), individual tree volume, conservation rate, stand volume per unit area, and annual increment, were investigated at 1.5, 2.5, and 5 years after pruning. At the same time, the chemical properties (organic matter, total nitrogen, total phosphorus, total potassium) and carbon sequestration capacity of Eucalyptus rhizosphere soil were analyzed. The results showed that at 5 years, the preservation rate of pruning below 1/2 tree height was the highest (83.75%), and the preservation rate of pruning below 2/3 tree height was the lowest (73.75%); at 1.5 years, pruning below 1/2 tree height significantly enhanced tree height, DBH and stand volume per unit area, though these effects diminished as the plantation aged. Pruning improved soil nutrient content (organic matter, total nitrogen, phosphorus, potassium) and soil quality. The pruning below 1/2 tree height treatment exhibited the highest carbon sequestration and oxygen production values at 1.5 and 2.5 years, but differences among treatments narrowed by 5 years. Moderate pruning (removing branches below 1/2 tree height) can enhance short-term growth, conservation rates, soil quality, and carbon sequestration capacity, but long-term benefits converge across treatments. It is recommended to adopt pruning intensities tailored to stand developmental stages and management goals to balance efficient plantation operations with ecological benefits.