Flexible multifunctional polymer-based electromagnetic interference (EMI) shielding composite films have important applications in the fields of 5G communication technology, wearable electronic devices, and artificial intelligence. Based on the design of a porous/multilayered structure and using polyimide (PI) as the matrix and polymethyl methacrylate (PMMA) microspheres as the template, flexible (Fe O /PI)-Ti C T -(Fe O /PI) composite films with controllable pore sizes and distribution of Ti C T hollow microspheres are successfully prepared by sacrificial template method. Owing to the porous/multilayered structure, when the pore size of the Ti C T hollow microspheres is 10 µm and the mass ratio of PMMA/Ti C T is 2:1, the (Fe O /PI)-Ti C T -(Fe O /PI) composite film has the most excellent EMI shielding performance, with EMI shielding effectiveness (EMI SE) of 85 dB. It is further verified by finite element simulation that the composite film has an excellent shielding effect on electromagnetic waves. In addition, the composite film has good thermal conductivity (thermal conductivity coefficient of 3.49 W (m·K) ) and mechanical properties (tensile strength of 65.3 MPa). This flexible (Fe O /PI)-Ti C T -(Fe O /PI) composite film with excellent EMI shielding performance, thermal conductivity, and mechanical properties has demonstrated great potential for applications in EMI shielding protection for high-power, portable, and wearable flexible electronic devices.