Abstract: Three-dimensional calculation is needed for high-temperature gas-cooled reactor (HTGR) to realize three-dimensional burn-up calculation, three-dimensional control rod calculation, power distribution reconstruction and ex-core detectors response analysis and etc. Because of the strong absorber in control rods and absorber balls region, the diffusion method can not be used directly. But transport method for detailed 3D model is very time-consuming. This paper proposes the procedure to homogenize the control rod region based on discontinuity factor theory, to calculate homogenized cross section and discontinuity factor by coupling 2D transport and diffusion calculation, then to realize 3D full core calculation with diffusion method corrected by discontinuity factor. It is shown through verification calculation that normal diffusion calculation is impossible to get accurate solution, and diffusion calculation corrected by discontinuity factor can reproduce the detailed transport solution not only in the neutron flux distribution but also in the eigenvalue and control rod worth, with much less computation time. Therefore the diffusion method with discontinuity factors is a nice solution to realize the three-dimensional calculation for HTGR.