Despite the importance of landscape design and water-resources management for urban planning, urban-forest transpiration was seldom estimated in situ. Detailed data on different urban trees’ water resource use and the effect of climatic fluctuations on their transpiration behaviour in different timescales are limited. In this study, we used a thermal dissipation method to measure the sap flux density (Js) of three urban tree species (Pinus tabulaeformis Carrière, Cedrus deodara (Roxb.) G. Don, and Robinia pseudoacacia Linn.) from 1 May 2008 to 30 April 2016 in Beijing Teaching Botanical Garden. The effects of environmental factors on sap flux density (Js) in different timescales were also analyzed. The results showed that there were significant differences in the sap flux density of three trees species in daily, seasonal, and interannual timescales. The hourly, seasonal, and interannual mean sap flux density of Pinus tabulaeformis were higher than that of Cedrus deodara and Robinia pseudoacacia. The seasonal mean Js of Pinus tabulaeformis, Cedrus deodara, and Robinia pseudoacacia in summer were 18.67, 16.19, and 41.62 times that in winter over 2008–2015. The annual mean sap flux density of Pinus tabulaeformis was 1.25–1.72 and 1.26–1.82 times that Cedrus deodara and Robinia pseudoacacia over 2008–2015. The Js responses in three tree species to environmental factors varied differently from daily to interannual timescales. The pattern of day-to-day variation in Js of three urban tree species corresponded closely to air temperature (Ta), soil temperature (Ts), solar radiation (Rs), and vapor pressure deficit (VPD). The Jarvis–Stewart model based on Ta, Rs, and VPD was more suitable for the sap flux density simulation of Pinus tabulaeformis than Cedrus deodara and Robinia pseudoacacia. The main factor affecting the sap flux density of Pinus tabulaeformis and Cedrus deodara was Ta in seasonal timescales. However, the main factor affecting the sap flux density of Robinia pseudoacacia was Ts. The interannual variations in the Js of Pinus tabulaeformis and Robinia pseudoacacia were mainly influenced by wind speed (w) and soil water content (SWC), respectively. The selected environmental factors could not explain the variation in the sap flux density of Cedrus deodara in an interannual timescale. The findings of the present study could provide theoretical support for predicting the water consumption of plant transpiration under the background of climate change in the future.