This study aimed to investigate the effects of increasing temperature on the transpiration rate and canopy conductance of soybean grown in temperature gradient chambers under drought and wet conditions. The heat balance method was used to measure the transpiration rate from sap flow; additionally, canopy conductance was continuously estimated from the transpiration rate and vapor pressure deficit (VPD). An increase of 3°C in temperature resulted in an increased transpiration rate but decreased canopy conductance. Further, the differences in canopy conductance observed at high and low temperature treatments were more remarkable during the morning than around noon. This suggested that there was concomitant increase in VPD with increasing temperature when solar radiation was low during the morning. Although the transpiration rate and canopy conductance decreased during drought conditions, the overall tendency of the response to the changes in temperature and VPD was similar to those in the well-watered condition. The partial correlation coefficients between canopy conductance and VPD were negative when the temperature effect was held constant. However, those between canopy conductance and temperature showed opposite trends in the two years of study—negative in 2011 but positive in 2012. These results suggest that the decrease of canopy conductance in a high temperature treatment is more likely caused by increasing VPD than by increasing temperature itself.