To illustrate the impact of trunk natural temperature gradient on sap flow velocity measured with thermal dissipation method, the trunk natural temperature gradient and heated temperature difference of Pinus tabulaeformis and Platycladus orientalis growing in low mountain areas around Beijing, together with weather and soil water conditions, were monitored daily and synchronously by using improved SF-L type thermal dissipation sap flow velocity measuring device and associated equipments from May 2007 to October 2007. The results showed that trunk natural temperature gradient of P. orientalis had greater impact on heated temperature difference than that of P. tabulaeformis. There was notable statistical difference (P<0.01) between the measurement results of sap flow velocity considering trunk natural temperature gradient and not. The average error percentage of sap flow velocity measurements caused by trunk natural temperature gradient was over 30%.The peak appeared when the solar altitudinal angle is low. Among the environmental factors, light intensity exerted the most significant influence on trunk natural temperature gradient, followed by air temperature. So the influence of trunk natural temperature gradient on the measurement results of sap flow velocity should not be neglected but be fully considered during study on water consuming mechanism of trees. Light intensity and air temperature are the two most significant factors influencing trunk natural temperature gradient, but the mechanism behind needs further research.