Abstract: The FMBEM (Fast Multipole Boundary Element Method) is applied to large scale numerical analysis of three-dimensional static thermal transfer problems. An introduction of the multipole expansion makes this algorithm applicable to perform boundary element analysis of thermal transfer problems with more than 300,000 unknowns on only one desktop computer. Mixed boundary conditions are achieved by using unified formulation of fundamental solutions. The Generalized Minimum Residue method is used as an iterative solver for the FMBEM. The computational efficiency of the FMBEM is tested in numerical examples. The results show that the FMBEM provides an order-of-magnitude increase in computational efficiency when compared with traditional solvers. This algorithm would be potential for the simulation of large scale thermal transfer analysis of complicated structures.