Compliant mechanisms are a new type of mechanism, designed to be flexible to achieve a specified motion as a mechanism. Such mechanisms can function as compliant thermal actuators in Micro-Electro Mechanical Systems (MEMS) by intentionally designing configurations that exploit thermal expansion effects in elastic material when appropriate portions of the mechanism structure are heated. This paper presents a new structural optimization method for the design of compliant thermal actuators based on the level set method and the Finite Element Method (FEM). First, an optimization problem is formulated that addresses the design of compliant thermal actuators considering the magnitude of the displacement at the output location. Next, the topological derivatives that are used when introducing holes during the optimization process are derived. Based on the optimization formulation and the level set method, a new structural optimization algorithm is constructed that employs the FEM when solving the equilibrium equations and updating the level set function. The re-initialization of the level set function is performed using a newly developed geometry-based re-initialization scheme. Finally, several design examples are provided to confirm the usefulness of the proposed structural optimization method.