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Intrinsic structural phase is a crucial foundation for the fundamental physical properties, and for creating innovative devices with unprecedented performances and unique functionalities. Long-range ferromagnetic orders of van der Waals CrI3 are strongly tied with interlayer stacking orders. However, the intrinsic structure of few-layer CrI3 still remains elusive; the predicted monoclinic phase has not yet been experimentally detected in bare few-layer CrI3. Here we uncover the intrinsic structure of few-layer CrI3 with interlayer antiferromagnetic coupling, which unambiguously show monoclinic stacking in both bare and hBN-encapsulated bilayer and tri-five-layer CrI3 throughout an entire temperature range from 300 to 10 K. An exotic spring damping effect from hBN encapsulation layers is experimentally observed in hBN/CrI3/hBN heterostructures, which partly hinders interlayer sliding of CrI3. This work demonstrates the intrinsic monoclinic crystal phase of few-layer CrI3 and associated correlation with magnetic orders, opening up numerous opportunities for creating magnetic texture by stacking design.