This paper derives the multi-layer heat conduction Green’s function, by integrating the eigen-expansion technique and the classic transmission line theories, and presents a logarithmic full-chip thermal analysis algorithm, which is verified by comparisons with a computational fluid dynamics tool (FLUENT). The paper considers Dirichlet’s and general heat convection boundary conditions at chip surfaces. Experimental results show that the algorithm offers superior computing speed, compared to FLUENT and traditional Green’s function based methods. The paper also studies the limitations of the traditional single-layer thermal model.