Polyimide is a potential material for high-performance printed circuit boards because of its chemical stability and excellent thermal and mechanical properties. Flexible printed circuit boards must have a low static dielectric constant and dielectric loss to reduce signal loss in high-speed communication devices. Engineering the molecular structure of polyimides with large pendant groups is a strategy to reduce their dielectric constant. However, there is no systematic study on how the large pendant groups influence electrical energy loss. We integrated all-atomic molecular dynamics and semi-empirical quantum mechanical calculations to examine the influence of pendant groups on polymer chain anisotropy and electrical energy loss at high frequencies. We analyzed the radius of gyration, relative shape anisotropy, dipole moment, and degree of polarization of the selected polyimides (TPAHF, TmBPHF, TpBPHF, MPDA, TriPMPDA, m-PDA, and m-TFPDA). The simulation results show that anisotropy perpendicular to chain direction and local chain rigidity correlate to electrical energy loss rather than dipole moment magnitudes. Polyimides with anisotropic pendant groups and significant local chain rigidity reduce electrical energy loss. The degree of polarization correlated well with the dielectric loss with a moderate computational cost, and difficulties in directly calculating the dielectric loss were circumvented.