This paper used poly (aryl ether ketone) (PAEK) resin with a low melting temperature to prepare laminate via the compression-molding process for continuous-carbon-fiber-reinforced composites (CCF-PAEK). Then, poly (ether ether ketone) (PEEK), or a short-carbon-fiber-reinforced poly (ether ether ketone) (SCF-PEEK) with a high melting temperature, was injected to prepare the overmolding composites. The shear strength of short beams was used to characterize the interface bonding strength of composites. The results showed that the interface properties of the composite were affected by the interface temperature, which was adjusted by mold temperature. PAEK and PEEK formed a better interfacial bonding at higher interface temperatures. The shear strength of the SCF-PEEK/CCF-PAEK short beam was 77 MPa when the mold temperature was 220 °C and 85 MPa when the mold temperature was raised to 260 °C. The melting temperature did not significantly affect the shear strength of SCF-PEEK/CCF-PAEK short beams. For the melting temperature increasing from 380 °C to 420 °C, the shear strength of the SCF-PEEK/CCF-PAEK short beam ranged from 83 MPa to 87 MPa. The microstructure and failure morphology of the composite was observed using an optical microscope. A molecular dynamics model was established to simulate the adhesion of PAEK and PEEK at different mold temperatures. The interfacial bonding energy and diffusion coefficient agreed with the experimental results.