Transition-metal trihalides MX3 (M = Cr, Ru; X = Cl, Br, and I) belong to a family of novel two-dimensional (2D) magnets that can exhibit topological magnons and electromagnetic properties, thus affording great promises in next-generation spintronic devices. Rich magnetic ground states observed in the MX3 family are believed to be strongly correlated to the signature Kagome lattice and interlayer van der Waals coupling raised from distinct stacking orders. However, the intrinsic air instability of MX3 makes their direct atomic-scale analysis challenging. Therefore, information on the stacking-registry-dependent magnetism for MX3 remains elusive, which greatly hinders the engineering of desired phases. Here, we report a nondestructive transfer method and successfully realize an intact transfer of bilayer MX3, as evidenced by scanning transmission electron microscopy (STEM). After surveying hundreds of MX3 thin flakes, we provide a full spectrum of stacking orders in MX3 with atomic precision and calculated their associated magnetic ground states, unveiled by combined STEM and density functional theory (DFT). In addition to well-documented phases, we discover a new monoclinic C2/c phase in the antiferromagnetic (AFM) structure widely existing in MX3. Rich stacking polytypes, including C2/c, C2/m, R3̅, P3112, etc., provide rich and distinct magnetic ground states in MX3. Besides, a high density of strain soliton boundaries is consistently found in all MX3, combined with likely inverted structures, allowing AFM to ferromagnetic (FM) transitions in most MX3. Therefore, our study sheds light on the structural basis of diverse magnetic orders in MX3, paving the way for modulating magnetic couplings via stacking engineering.