Shear and thermal processing can greatly influence nanoparticles’ orientation and dispersion, affecting the nanocomposites’ conductivity and mechanical properties. The synergistic effects of shear flow and Carbon nanotubes (CNTs) nucleating ability on the crystallization mechanisms have been proven. In this study, Polylactic acid/Carbon nanotubes (PLA/CNTs) nanocomposites were produced by three different molding methods: compression molding (CM), conventional injection molding (IM), and interval injection molding (IntM). Solid annealing at 80 °C for 4 h and pre-melt annealing at 120 °C for 3 h was applied to research the CNTs’ nucleation effect and the crystallized volume exclusion effect on the electrical conductivity and mechanical properties. The volume exclusion effect only significantly impacts the oriented CNTs, causing the conductivity along the transverse direction to rise by about seven orders of magnitude. In addition, the tensile modulus of the nanocomposites decreases with the increased crystallinity, while the tensile strength and modulus decrease.