Transient heat conduction analysis of the functionally graded structures is of great importance for the structure design and manufacturing. In this study, 2D heat conduction problem is solved by the meshless smoothed particle hydrodynamics (SPH) method. To improve the computational accuracy and efficiency of traditional SPH method, a symmetric SPH approach is adopted, which can calculate a function and its derivatives of higher order using one symmetric matrix. The heat conduction function is discretized by the improved SPH method, as well as the boundary conditions. The SPH analysis of the heat conduction in several functionally graded structures with different geometries is performed and validated by the analytical values and the FEM results in literature. The effect of the graded index on the temperature distribution in the structure domain is also studied. The present paper provides an alternative potential method for the heat conduction analysis of functionally graded materials.