To prepare PIs (polyimides) with desirable thermal and mechanical properties is highly demanded due to their widespread applications in flexible optoelectronic devices and printed circuit boards. Here, the PI films of BPDA/4,4′-ODA, BPDA/3,4′-ODA, PMDA/4,4′-ODA, PMDA/3,4′-ODA systems were prepared, and it was found that the PIs with 3,4′-ODA always exhibit a high modulus compared with the PIs with 4,4′-ODA. To disclose the mechanism of high-modulus PI films with 3,4′-ODA, amorphous PI models and uniaxial drawing PI models were established and calculated based on MD simulation. The PI structural deformations at different length scales, i.e., molecular chain cluster scale and repeat unit scale, under the same stress were detailed and analyzed, including the variation of chain conformation, bond length, bond angle, internal rotation energy, and torsion angle. The results indicate that PIs with 3,4-ODA have higher internal rotation energy and smaller deformation with the same stress, consistent with the high modulus.