In the present study a three-dimensional (3-D) transient inverse heat conduction problem is solved using the conjugate gradient method (CGM) and the general purpose commercial code CFX4.2-based inverse algorithm to estimate the unknown boundary heat flux in any 3-D irregular domain. The advantage of calling CFX4.2 as a subroutine in the present inverse calculation lies in that many difficult but practical 3-D inverse problems that can be solved under this construction. Results obtained by using the conjugate gradient method to solve these 3-D inverse problems are justified based on the numerical experiments. It is concluded that accurate boundary fluxes can be estimated by the CGM except for the final time. The reason and improvement of this singularity are addressed. Finally, the effects of the measurement errors on the inverse solutions are discussed.