Carbon–carbon (C–C) composites are highly sought-after in aviation, automotive, and defense sectors due to their outstanding thermal and thermo-mechanical properties. These composites are highly valued for their exceptional thermal and thermo-mechanical properties, including remarkably low density and coefficient of thermal expansion, which are expected to surpass those of many alloys and other composites in the production of high-grade components. However, the current manufacturing methods for C–C composites are unable to meet market demands due to their high cost, low production speed, and labor-intensive processes, limiting their broader applications. This study presents an innovative approach by introducing a new extrusion-based 3D printing method using multiphase direct ink writing (MDIW) for C–C composite fabrication. The primary matrix utilized is a phenol-formaldehyde thermosetting resin, reinforced with silicon carbide (SiC) and graphite nanopowder (Gnp), focusing on achieving simple, scalable, and environmentally sustainable production of green parts with enhanced polymer matrix. This is followed by an inert carbonization process to obtain the final C–C composites. The research emphasizes the careful optimization of curing and rheological properties, including the use of suitable viscosity modifiers like carbon black (CB). Furthermore, the MDIW process demonstrates its capability to pattern dual nanoparticles within the composite structure in a well-ordered manner, leading to improved overall performance. Thermo-mechanical and thermo-electrical properties were thoroughly tested, showcasing the multifunctionality of the composite for diverse applications, from high-value industries like aerospace to broader uses such as heatsinks and electronic packaging.