The intrinsic coupling effect between the multiscale microstructure and macroscopic performance is a fundamental issue in polymer engineering and polymer physics. Combing the tensile testing and in situ wide-angle X-ray diffraction, the stretching-induced polymorphic transformation from tetragonal form II into hexagonal form I in the butene-1/1,5-hexadiene random copolymers was studied in this work. The mechanical response and crystallite evolution of the designed copolymers with various co-unit concentrations were combined to reveal the interplay between macroscopic stretching and microscopic phase transition for the whole deformation process. The results show that the elastic deformation does not change the structure significantly and it is the yield that triggers the II-I phase transition, which happens at a comparable strain of around 0.06 for all polymers studied. It was indicated that yield destroys the crystallite skeleton that bears the external stretching in the elastic deformation region and the generation of new tie chains enhances the stress transfer into lamellae, triggering the II-I phase transition. The generation of more transformed form I improves the stretching strength, and the increased stress is also required to ensure the proceeding of phase transition. A direct correspondence was established between the transition kinetics and true stress for the course of the II-I phase transition. Furthermore, after phase transition, the transformed form I increases the modulus of the molecular network by 2 orders of magnitude with respect to that of the original form II. This indicates that the crystallite acts as the physical cross-links for the molecular network and the enhancement of strain hardening is strongly dependent on the crystal modification.