The mathematical model of steady heat transfer analysis for orthotropic structure is established based on Element-Free Galerkin (EFG) method and the essential boundary conditions are enforced using penalty method. The reliability of heat transfer model and MATLAB programs have been verified through three engineering examples in practice. The effects of nodes distribution pattern, scaling factors, penalty factors and weight functions on the EFG temperature results of different orthotropic structures are evaluated. A comparison of the CPU computing time between EFG and FEM is also studied. By comparison with finite element temperature and temperature gradient, it is revealed that the temperature based on EFG has higher calculation precision for steady heat transfer problem, and the temperature is not affected by nodes distribution pattern. The rational values of scaling factors and penalty factors are provided respectively. In addition, the computational relative error increases with the decrease of the orthotropic factor during various weight functions, and the cubic spline and parabola weight functions are the preferred choices in the heat transfer analysis of the orthotropic structure.