Using Granier-type thermal dissipation probes, sap flow velocity (V) of two species (Cunninghamia lanceolata, Symplocas setchuensis) were monitored in three depths (10mm, 30mm, 50mm) of xylem from July to September, 2015, at Jinyun Mountain of Chongqing to analyze the radial variations of V and estimate trees transpiration accurately. The results showed that the radial pattern of V for Cunninghamia lanceolata was: V30～50mm＞V10～30mm＞V0～10mm. V30～50mm was 1.65 times of V0～10mm and V10～30mm was 1.12 times of V0～10mm. The radial pattern of V for Symplocas setchuensis was: V10～30mm＞V0～10mm≈V30～50mm. V10～30mm was about 2.6 times of V0～10mm and V30～50mm; There were significant liner relationships between every two depths; The daily variations of V in three depths of xylem displayed unimodal or bimodal curves; The value of V was highest in July and the transpiration was stopped in noon. There were temporal and spatial differences in start time and peak time of sap flow, which was earlier in July than in August and September. The start time was earliest and the peak time was latest at the plot where V was maximal in radial xylem. The daily transpiration of Cunninghamia lanceolata and Symplocas setchuensis were 7274.815g and 12481.494g, estimated by different V in different depths. The error by omitting radial variations in V were 9.83%～17.89% for Cunninghamia lanceolata and 42.41%～66.88% for Symplocas setchuensis, its coefficient of variation (CV) were 26%～45% and 19%～26%.