To treat critical-sized defects in long bones, a novel structure was proposed by introducing a Haversian biomimetic structure and trabecular-like irregular pore morphology (IPM) structure into functional gradient porous scaffolds (FGPS). The outer shell structure is a "hard" structure providing mechanical support, and the inner core is a "soft" structure with radial gradient distribution IPM structure to promote the ingrowth of bone tissue. In this study, different inner core continuous gradient FGPS (GIPM) and layered FGPS (IPM, and BCC structure), with different outer shell pore sizes (300, 500, and 700 μm) were designed and fabricated by selective laser melting. The results show the stiffness of those FGPS was between 20.0-28.7 kN/mm, which is similar to the native femur (with a stiffness ranging from 7.2-11.7 kN/mm) of similar size. The GIPM-500 has more uniform stress distribution and stress transfer, resulting in superior load-bearing efficiency. Moreover, GIPM-500 exhibited excellent fatigue durability, achieving excellent fatigue cycles of more than 1×106 cycles. Cell immunofluorescence shows that the GIPM-500 and IPM-500 are more suitable for cell attachment and growth due to the flexibility of the local porosity and curvature. Bone defect repair simulations showed that GIPM-500 can meet normal load-bearing requirements while having little impact on the normal stress-strain trajectory. This work provides a novel biomimetic scaffold design containing both cortical and trabecular bone components for repairing critical-size defects in long bones.