Due to the component advantages and structural features, poly(3,4-ethylenedioxythiophene):poly(styrenesulfonic acid) (PEDOT:PSS) based inorganic–organic composite films shows huge application potential in various fields. However, there are few reports on the bi-functions of thermoelectric (TE) and electromagnetic interference (EMI) shielding for the PEDOT:PSS-based functional films. Herein, metal–organic frameworks (MOFs)-derived BixSey@C sheets with average size about ∼ 7.32 μm are obtained via the solvothermal reaction and selenization pyrolysis treatment, and then flexible free-standing BixSey@C/PEDOT: PSS (BSCP) composite films are obtained by a feasible vacuum filtration combined with cold pressing treatment, using different contents of BixSey@C content as inorganic component. Micrometer BixSey@C sheets are uniformly dispersed in the PEDOT:PSS matrix constructing bi-functional composite films with unique layered structure. When the MOFs-derived BixSey@C content is 70%, BSCP-70 composite film gets a power factor of 11.23 μW m−1 K−2 at 340 K. Meanwhile, the BSCP-70 composite film reaches the highest average total EMI shielding effectiveness (SET) value of 45.0 dB at only 41.9 μm thickness at X-band. Based on multi-physical properties of MOF-derived BixSey@C and PEDOT:PSS, flexible BixSey@C/PEDOT:PSS composite films display good application potentiality in the flexible TE devices and EMI shielding protection.