The sequence and coupling of intra-and interchain orderings in flow-induced crystallization (FIC) of partially cross-linked isotactic polypropylene (iPP) is studied with in situ Fourier transform infrared spectroscopy (FTIR) and synchrotron radiation X-ray scattering techniques, which reveal that multiscale structural intermediates emerge prior to the onset of crystallization. Upon imposing flow, intrachain conformational ordering or coil helix transition (CHT) occurs first, which is directly correlated with external stress. As helical content is built up at large strain, density fluctuation happens, and sufficient long helices may result in orientation ordering before FIC. The results demonstrate that stress induced intrachain CHT is the essential structural intermediate in FIC, which can be further coupled with interchain orientation and density providing either helical content or length meets the criterions for the phase transitions. We propose that coupling among external stress, intrachain conformational, and interchain orientation and density orderings to be the molecular mechanism for FIC of polymer forming helical structures.