Abstract Thermoplastic matrices are necessary in 3D printing of continuous fiber reinforced composites (CFRC) as a binder, but their high viscosity is not conducive to the impregnation of fibers. A two‐matrix printing is proposed via simultaneously employing thermoplastic and thermosetting matrices, making full use of the great impregnation of thermosetting resin. However, there is no systematic comparative study on the mechanical properties of 3D printed CFRC between two‐matrix and single‐matrix. The focus of this study is to systematically explore differences between 3D printed two‐matrix and single‐matrix composites. Two‐matrix composites and single‐matrix composites were prepared by Fused Deposition Modeling (FDM) technology. The microstructure and fracture morphology of the printed samples were characterized by using an optical microscope (OM) and an image measuring instrument. A novel method utilizing Peridynamics (PD) theory has been proposed for the simulation of fracture patterns and failure mechanisms. The interfacial energy of carbon fiber and matrix was analyzed via a molecular dynamics method. The experimental findings demonstrate that the carbon fibers are well impregnated by the thermosetting resin in two‐matrix composites, having fewer voids than single‐matrix composites. The normalized tensile strength of the 3D printed two‐matrix composites is 46.24% higher than that of the single‐matrix composites. The interfacial energy in two‐matrix composites is higher, showing a better binding and a stronger synergistic effect between carbon fiber monofilaments. The PD model well captures the fracture characteristics. The results of this paper are significant in comparing the properties of single‐matrix and two‐matrix composites and explaining the reasons for the differences. Highlights The two‐matrix composites have better mechanical properties than single‐matrix composites. The two‐matrix composites exhibit significantly greater interfacial energy compared to single‐matrix composites. The two‐matrix composites are better impregnated with a more uniform distribution of binder. The PD model well captures the fracture characteristics.