Electrically conductive segregated networks were formed in carbon nanotube (CNT)/poly(lactic acid) (PLA) composite, in which CNTs are selectively located in poly(l-lactide) (PLLA) continuous phase and the continuous phase forms completed conductive networks at PLA stereocomplex crystallites (PLAsc) domain interfaces. The segregated CNT/PLLA/PLAsc composite with only 2.0 wt % CNT already exhibits an average electromagnetic interference (EMI) shielding effectiveness (SE) of 36 dB, which is 90% higher than that for the conventional CNT/PLLA composite with the same CNT loading. Owing to the high interfacial adhesion between PLLA and PLAsc, the tensile strength of the CNT/PLA composite reaches 65.2 MPa, which is 52% higher than the 41.8 MPa measured for pure PLAsc. Our work provides a novel way to develop a CNT/PLA composite with simultaneous high-performance EMI shielding and superior mechanical properties.