Water is a vital resource for tree growth, and changes in plantation and canopy structure can affect stand transpiration (Ec), consequently influencing water use efficiency (WUE). Populus tomentosa is a fast-growing and productive timber species in China. In recent years, thinning combined with pruning has become a widely used silvicultural practice for timber management. However, its effect on water utilization has been less well studied. To address this gap, we designed experiments with two thinning intensities and three pruning treatments. Thermal dissipation probes were employed to monitor tree sap flow density (Js), and estimated Ec and canopy conductance (gc). We established a relationship between the canopy transpiration per unit leaf area (EL) and gc and climatic factors. Finally, we compared basal area increment (BAI) and WUE among treatments under different rainfall conditions. The results indicated that: (1) The pattern of transpiration changes was consistent at both the individual tree and stand level. (2) The combined effect of T1 (thinning intensity of 833 trees per hectare) and pruning reduced Ec, decreasing the sensitivity of tree transpiration to the climate, with no discernible impact on EL and gc. Conversely, T2 (thinning intensity of 416 trees per hectare) and pruning increased EL and gc but had no effect on Ec, enhancing the sensitivity of tree transpiration to the climate. The sensitivity of gc to VPD suggested a flexible stomatal regulation of transpiration under different combined thinning and pruning treatments. (3) Under T1, only P2 (4 m pruning from ground) promoted WUE, while pruning effects significantly reduced WUE under T2. Overall, the WUE of T2P0 (thinning intensity of 416 trees per hectare combined with no pruning) was significantly higher than that of the other treatments, and that of T1P0 (thinning intensity of 833 trees per hectare combined with no pruning) was significantly lower than that of the other treatments. Additionally, significant differences in Ec and BAI were observed among treatments under different rainfall conditions, with the promotion effect of Ec on BAI being more pronounced in the dry season.