A nano-sandwich construct was built by combining two-dimensional graphene nanosheets (GNSs) and one-dimensional carbon nanotubes (CNTs) to improve the mechanical properties of hydroxyapatite-polyetheretherketone (HAP-PEEK) scaffolds for bone tissue engineering. In this nano-sandwich construct, the long tubular CNTs penetrated the interlayers of graphene and prevented their aggregation, increasing the effective contact area between the construct and matrix. The combination of GNSs and CNTs in a weight ratio of 2:8 facilitated the dispersion of each other and provided a synergetic effect in enhancing the mechanical properties. The compressive strength and modulus of the scaffolds were increased by 63.58% and 56.54% at this time compared with those of HAP-PEEK scaffolds, respectively. The carbon-based fillers, pulling out and bridging, were also clearly observed in the matrix. Moreover, the dangling of CNTs and their entangling with GNSs further reinforced the mechanical properties. Furthermore, apatite layer formed on the scaffold surface after immersing in simulated body fluid, and the cells attached and spread well on the surface of the scaffolds and displayed good viability, proliferation, and differentiation. These evidence indicate that the HAP-PEEK scaffolds enhanced by GNSs and CNTs are a promising alternative for bone tissue engineering.