The flame retardants and electromagnetic interference (EMI) shielding performance were enhanced by using imidazolium-functionalized polyurethane (IPU) modified multi-walled carbon nanotubes (CNTs) and ammonium polyphosphate (APP) for polylactic acid (PLA)/polycaprolactone (PCL) composites. The PLA/PCL/10APP/8CNT/1.6IPU composite containing 10 wt% APP and 8 wt% imidazolium modified CNTs reached the limiting oxygen index (LOI) value of 30.3 % and passed the V-0 rating in UL-94 tests. Moreover, the peak of the heat release rate (pHRR) and total heat release (THR) for this composite reached around 302 kW/m2 and 64 KJ/m2, which were decreased by 39.1 % and 15.8 % compared with that of PLA/PCL/10APP composite. The improved flame retardancy was attributed to the interplay of catalytic, barrier, and condensed char forming of imidazolium-modified CNTs and APP. IPU catalyzed the charring effect of the polymer matrix during combustion and regulated the migration of more CNTs to disperse at the two-phase interface. The dispersion of imidazolium-modified CNTs and co-continuous phase structure of the composites can establish continuous conductive pathways. The PLA/PCL/APP/CNT/IPU composite obtained a higher conductivity compared to the PLA/PCL/APP/CNT composite and whose EMI SE reached 33.9 dB, which is a promising candidate for next-generation sustainable and protective plastics.