The optimization of flame retardancy and thermal conductivity in epoxy resin (EP), utilized in critical applications such as mechanical components and electronics packaging, is a significant challenge. This study introduces a novel, ultrasound-assisted self-assembly technique to create a dual-functional filler consisting of carbon nanotubes and ammonium polyphosphate (CNTs@APP). This method, leveraging dynamic ligand interactions and strategic solvent selection, allows for precise control over the assembly and distribution of CNTs on APP surfaces, distinguishing it from conventional blending approaches. The integration of 7.5wt.% CNTs@APP10 into EP nanocomposites results in substantial improvements in flame retardancy, as evidenced by a limiting oxygen index (LOI) value of 31.8% and achievement of the UL-94V-0 rating. Additionally, critical fire hazard indicators, including total heat release (THR), total smoke release (TSR), and the peak intensity of CO yield (PCOY), are significantly reduced by 45.9% to 77.5%. This method also leads to a remarkable 3.6-fold increase in char yield, demonstrating its game-changing potential over traditional blending techniques. Moreover, despite minimal CNTs addition, thermal conductivity is notably enhanced, showing a 53% increase. This study introduces a novel approach in the development of multifunctional EP nanocomposites, offering potential for wide range of applications.