Abstract: The Japanese research reactor JRR3M which had strong absorber assemblies was studied. The angular flux discontinuity factor (AFDF) was defined when the transport calculation in JRR3M was processed. For improving calculation precision and making the AFDF self-consistent, the iteration method was used. Super cell approximation method was used for big calculation quantity of reactor core design, and it could reduce calculation time efficiently and had strong maneuverability. Using assembly flux shape function, the homogeneous fluxes were reshaped and made them adjacent to the heterogeneous fluxes distribution. Finally, how to choose AFDFs in diffusion calculation and transport calculation was studied. The result shows that different AFDFs are chosen according to different reference models.