To analyse the influence of a bifurcation structure on the heat transfer and temperature distribution of pulsatile blood flow, a transient heat transfer model of pulsatile blood flow was constructed. The velocity and temperature distributions of pulsatile blood flow in a bifurcation vessel tree that included a main blood vessel and two branch vessels were simulated using the model. The transient Nusselt number and the time-averaged Nusselt number in branch vessels with different diameters or different boundary conditions were calculated and compared. The results show that the temperature and velocity profiles at the inlet cross section of the branch vessels are non-axisymmetric and pulsatile. There is a low temperature region at the bifurcation junction of the two branch vessels, and the transient value of the minimum temperature varies with the time of the pulsatile blood flow. Comparing the simulated Nusselt number of pulsatile blood in this study with that of steady-state laminar blood reported in the literature, we found that pulsation does not enhance the heat transfer of blood flow. For the real vessel parameters in a physiological system, the time-averaged Nusselt number in branch vessels, especially for large vessels, is larger than the Nusselt numbers of a fully developed laminar flow for blood. The asymptotic values of the Nusselt number of blood for a uniform heat flux and uniform wall temperature are 4.432 and 3.753, respectively. (C) 2017 Elsevier Ltd. All rights reserved.