High-performance electromagnetic interference (EMI) shielding materials with ultralow density and environment friendly properties are greatly demanded to address electromagnetic radiation pollution. Herein, carbon nanotubes/polylactic acid (CNTs/PLA) materials with different CNTs contents, which exhibit characteristics of light weight, environmental protection and good chemical stability, are fabricated by 3D printing technology, where CNTs are evenly distributed and bind well with PLA. The performances of 3D printed CNTs/PLA composite are improved compared to pure 3D printed PLA composite, which include mechanical properties, conductive behaviors and electromagnetic interference (EMI) shielding. The EMI shielding effectiveness (SE) of CNTs/PLA composite could be improved when the contents of CNTs increase. When it reaches 15 wt%, the EMI SE of 3D printed CNTs/PLA composite could get up to 47.1 dB, which shields 99.998% of electromagnetic energy. Meanwhile, the EMI shielding mechanism of 3D printed CNTs/PLA composite is mainly of absorption loss, and it generally accounted for more than 80% of the total shielding loss. These excellent comprehensive performances endow the 3D printed CNTs/PLA composite with great potential for use in industrial and aerospace area.