Vast amounts of electromagnetic waves are generated in modern society, which severely endanger human health and cause instrument disturbance. Furthermore, practical application of electromagnetic shielding polymer-based materials aspires to flame retardancy. Herein, cellulose acetate butyrate modified ammonium polyphosphate (CAPP) and phosphoramide flame retardant decorated short carbon fiber (MSCF) were synthesized separately and then simultaneously blended into thermoplastic polyurethane (TPU) to prepare a series of flame retardant TPU composites. Then, the multi-hierarchical flexible TPU/CAPP/MSCF composites were fabricated via our self-developed air-assisted thermocompression method. The results revealed that the TPU/CAPP/MSCF showed improved thermal stability. Moreover, the TPU/10CA/2.5F incorporated with 10.0 wt.% CAPP and 2.5 wt.% MSCF respectively exhibited 77.8% and 58.6% reduction in peak of heat release rate (PHRR) and total heat release (THR), compared to those of pure TPU. In addition, the TPU/10CA/2.5F passed the UL-94 V-0 rating test and achieved a higher limit oxygen index (LOI) (27.3%) than pure TPU (21.7%). In the case of electromagnetic interference shielding effectiveness (EMI SE), the TPU/10CA/10.0F-SW with 10 wt.% CAPP and 10 wt.% MSCF dispersed in the surface layer and Ti₃C₂T_x MXene intercalated in the interlayer exhibited EMI SE of 43.8 dB in X band and 32.0 dB in K band. Summarily, synergistic effect between CAPP and MSCF together with scattered and multiply adsorbed effect of MSCF, MXene and CAPP was responsible for fire safety and EMI shielding property improvements. This work provides a fascinating strategy for fabricating multi-hierarchical flexible TPU composites with outstanding flame retardant and EMI shielding performances.