Combining recycled carbon fiber (rCF) and 3D printing technology has shown great potential for fabricating functional prototypes and production parts used in the aerospace and automotive industries. However, it is still a challenge to design flame-retardant 3D printed parts with high mechanical properties and flame-retardant rating. In the work, a flame-retardant polyamide (PA)-based composite for material extrusion 3D printing was prepared by utilization of rCF, polyhedral oligomeric silsesquioxanes (POSS), and 9,10-Dihydro-9-oxa-10-phosphaphenanthrene (DOPO)-based flame retardant. The 3D-printed composites have high thermal stability, mechanical properties, and excellent flame retardancy with a V-0 rating. With the benefits of material extrusion 3D printing, directionally arranged rCF in 3D printed composites could effectively inhibit the fire spread, extend the time to ignition (TTI), reduce the total heat release (THR) and total smoke release (TSR) of 3D printed composites. The directional flame-retardant mechanism is mainly the thermal conductivity mechanism of the condensed phase and the promotion of stable ordered carbon layer formation. It provides a promising path for designing high-performance flame-retardant materials.