A dodecahedral superstructure consisting of a single layer of Janus spheres containing ZIF‐67 nanodots is prepared by in situ polymerization, with ZIF‐67 and bio‐based phytic acid (PA) as templates and dopants. It is used to improve the flame retardant, electromagnetic (EMI) shielding, and thermal conductivity properties of polyurea (PUA). By adding 5 wt% polyaniline@cobalt phytate‐2.0 (PANI@Co‐PA‐2.0), the peak of heat release rate and the peak of smoke production rate are reduced by 54.9 and 59.9%, respectively. The peak of CO and CO2 production also decreased by 46.2 and 53.1%, respectively. A decrease in the absorption intensity of aliphatic and aromatic volatiles is also observed. The fire safety of PUA is greatly improved. In addition, PUA/PANI@Co‐PA‐2.0 exhibits an EMI shielding capability of 22.4 dB with the help of reduced graphene oxide, which confirms the possibility of PUA material application in the field of electromagnetic shielding. The 5 wt% filler increases the tensile strength of the PUA matrix to 6.3 MPa, and the composite material obtains good thermal conductivity. This work provides a viable method for the preparation of a flame‐retardant, conductive, and electromagnetic refractory PUA substrate.