In this work, an improved parallel SPH method is proposed to accurately solve the three-dimensional (3D) transient heat conduction equation with variable coefficients. The improvements are described as follows. Firstly, the first-order symmetric smoothed particle hydrodynamics (SPH) method is extended to the simulating of the 3D problem based on Taylor expansion. Secondly, the concept of stabilized up-wind technique is introduced into the convection term. Thirdly, the MPI parallel technique based on the neighboring particle mark method is introduced into the above improved SPH method, and named the corrected parallel SPH method for 3D problems (CPSPH-3D). Subsequently, the accuracy, convergence and the computational efficiency of the proposed CPSPH-3D method are tested by simulating the 3D transient heat conduction problems with constant/variable coefficient, and compared with the analytical solution. Meanwhile, the capacity of the proposed CPSPH-3D for solving the 3D heat conduction problems with the Dirichlet and Newmann boundaries is illustrated, in which the change of temperature with time under the complex cylindrical area is also considered. The numerical results show that:1) the proposed CPSPH-3D method has the better stability, higher accuracy and computational efficiency than the conventional SPH method no matter whether the particle distribution is uniform; 2) the calculating time can be well reduced by increasing the number of CPUs when the particle number is refined in the simulations of CPSPH-3D. Finally, the temperature variation in the 3D functionally gradient material is predicted by the corrected parallel SPH method, and compared with the other numerical results. The process of temperature variation in the functionally gradient material can be shown accurately.