Rectangular-shaped and disk-shaped heat pipes, as innovative heat sinks, are investigated to optimize the thermal performance of three-dimensional integrated circuits (3D ICs) in this work. Finite volume numerical analysis is employed to carry out the simulation of the thermal performance of 3D ICs. Both rectangular-shaped and disk-shaped heat pipes substantially improved the overall thermal performance and reduced the hotspot temperatures by 7 K and 11 K on average, respectively. Furthermore, utilizing the rectangular-shaped or the disk-shaped heat pipe as the heat spreader in place of a solid copper heat spreader further optimizes the thermal performance by reduction of the junction temperatures 14 K and 16 K on average, respectively. These reductions are achieved while the weight of the setup is also significantly reduced. The results indicate that the innovative flat-shaped heat pipes significantly optimize the thermal performance of 3D ICs. The model and results presented in this work aim to pave the way to markedly alleviate the thermal issues of the 3D ICs.